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Ytterbium in PDB 8f7n: Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain

Protein crystallography data

The structure of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain, PDB code: 8f7n was solved by S.Salar, F.D.Schubot, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.60 / 2.70
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 184.33, 184.33, 113.36, 90, 90, 90
R / Rfree (%) 24.4 / 26

Ytterbium Binding Sites:

The binding sites of Ytterbium atom in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain (pdb code 8f7n). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 10 binding sites of Ytterbium where determined in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain, PDB code: 8f7n:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Ytterbium binding site 1 out of 10 in 8f7n

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Ytterbium binding site 1 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 1 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb501

b:80.7
occ:0.50
 OE2 A:GLU137 2.3 90.3 1.0
CD A:GLU137 3.0 96.3 1.0
OE1 A:GLU137 3.4 81.8 1.0
HG3 A:GLU137 4.1 98.3 1.0
CG A:GLU137 4.1 79.2 1.0
HH12 A:ARG144 4.1 93.9 1.0
OD1 A:ASP141 4.1 79.7 1.0
HG2 A:GLU137 4.4 98.3 1.0
NH1 A:ARG144 4.4 75.5 1.0
HH22 A:ARG144 4.6 102.1 1.0
OD2 A:ASP141 4.6 80.6 1.0
HH11 A:ARG144 4.7 93.9 1.0
CG A:ASP141 4.8 74.2 1.0
CZ A:ARG144 4.8 75.4 1.0
NH2 A:ARG144 4.9 82.3 1.0

Ytterbium binding site 2 out of 10 in 8f7n

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Ytterbium binding site 2 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


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Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb502

b:93.9
occ:0.32
 YB A:YB503 1.7 208.5 1.0
YB A:YB507 3.7 181.4 0.0
HE1 A:HIS210 4.3 91.2 1.0
OE2 A:GLU193 4.8 139.4 1.0

Ytterbium binding site 3 out of 10 in 8f7n

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Ytterbium binding site 3 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 3 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb503

b:208.5
occ:1.00
 YB A:YB502 1.7 93.9 0.3
YB A:YB507 2.1 181.4 0.0
OE2 A:GLU193 3.1 139.4 1.0
YB A:YB504 3.8 176.8 0.0
CD A:GLU193 3.9 102.4 1.0
OE1 A:GLU193 3.9 92.7 1.0
YB A:YB508 4.0 99.4 0.0
HE1 A:HIS210 4.2 91.2 1.0

Ytterbium binding site 4 out of 10 in 8f7n

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Ytterbium binding site 4 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 4 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb504

b:176.8
occ:0.00
 YB A:YB507 2.0 181.4 0.0
OE2 A:GLU193 3.4 139.4 1.0
YB A:YB503 3.8 208.5 1.0
CD A:GLU193 4.6 102.4 1.0
YB A:YB508 4.8 99.4 0.0

Ytterbium binding site 5 out of 10 in 8f7n

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Ytterbium binding site 5 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 5 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb505

b:428.9
occ:0.66
 OE2 A:GLU75 3.4 184.3 1.0
CD A:GLU75 4.4 170.3 1.0
YB A:YB506 4.7 444.9 0.7
OE1 A:GLU75 4.7 198.2 1.0

Ytterbium binding site 6 out of 10 in 8f7n

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Ytterbium binding site 6 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 6 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb506

b:444.9
occ:0.72
 OE2 A:GLU75 4.6 184.3 1.0
YB A:YB505 4.7 428.9 0.7
HH11 A:ARG78 4.7 139.7 1.0
HH12 A:ARG78 4.9 139.7 1.0

Ytterbium binding site 7 out of 10 in 8f7n

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Ytterbium binding site 7 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 7 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb507

b:181.4
occ:0.00
 YB A:YB504 2.0 176.8 0.0
YB A:YB503 2.1 208.5 1.0
OE2 A:GLU193 2.3 139.4 1.0
CD A:GLU193 3.4 102.4 1.0
YB A:YB502 3.7 93.9 0.3
OE1 A:GLU193 3.9 92.7 1.0
YB A:YB508 4.2 99.4 0.0
HG2 A:GLU193 4.6 108.8 1.0
CG A:GLU193 4.6 87.9 1.0
HG3 A:GLU193 4.9 108.8 1.0

Ytterbium binding site 8 out of 10 in 8f7n

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Ytterbium binding site 8 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 8 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb508

b:99.4
occ:0.00
 HA A:GLU189 2.5 82.4 1.0
HG3 A:GLU193 2.8 108.8 1.0
OE2 A:GLU193 2.9 139.4 1.0
CB A:GLU189 3.0 58.7 1.0
CA A:GLU189 3.1 65.9 1.0
CD A:GLU193 3.2 102.4 1.0
CG A:GLU193 3.5 87.9 1.0
O A:GLU189 3.5 69.5 1.0
HB A:THR192 3.6 82.3 1.0
C A:GLU189 3.8 68.8 1.0
OE1 A:GLU193 3.9 92.7 1.0
HG2 A:GLU193 3.9 108.8 1.0
YB A:YB503 4.0 208.5 1.0
YB A:YB507 4.2 181.4 0.0
N A:GLU189 4.4 68.5 1.0
HG22 A:THR192 4.5 82.2 1.0
CB A:THR192 4.5 65.8 1.0
HB2 A:GLU193 4.6 96.8 1.0
HG21 A:THR192 4.6 82.2 1.0
H A:GLU193 4.7 85.1 1.0
CB A:GLU193 4.7 77.9 1.0
YB A:YB504 4.8 176.8 0.0
H A:GLU189 4.8 85.5 1.0
CG2 A:THR192 4.8 65.7 1.0
HG1 A:THR192 4.8 89.5 1.0
O A:ALA188 5.0 68.3 1.0

Ytterbium binding site 9 out of 10 in 8f7n

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Ytterbium binding site 9 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 9 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb509

b:131.8
occ:0.31
 HE A:ARG164 2.3 118.7 1.0
HH21 A:ARG164 2.9 123.1 1.0
NE A:ARG164 3.1 96.1 1.0
NH2 A:ARG164 3.6 99.8 1.0
HD3 A:ARG164 3.7 98.2 1.0
CZ A:ARG164 3.8 107.5 1.0
OE1 A:GLU167 3.8 106.6 1.0
CD A:ARG164 4.0 79.0 1.0
HD2 A:ARG164 4.2 98.2 1.0
HH22 A:ARG164 4.3 123.1 1.0
HE22 A:GLN160 4.5 127.6 1.0
HG11 A:VAL163 4.7 110.9 1.0
OE2 A:GLU299 4.8 117.1 1.0
CD A:GLU167 4.9 100.4 1.0
HG13 A:VAL163 5.0 110.9 1.0

Ytterbium binding site 10 out of 10 in 8f7n

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Ytterbium binding site 10 out of 10 in the Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 10 of Crystal Structure of Chemoreceptor Mcpz Ligand Sensing Domain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Yb510

b:772.0
occ:1.00
 OD1 A:ASP403 2.8 201.9 1.0
OD2 A:ASP403 3.0 205.0 1.0
CG A:ASP403 3.2 200.2 1.0
OE1 A:GLU399 4.3 224.9 1.0
HB1 A:ALA109 4.6 198.4 1.0
CB A:ASP403 4.6 190.4 1.0
HA A:ASP403 4.7 224.7 1.0
HB3 A:ASP403 4.8 231.8 1.0
HB2 A:GLU399 4.9 193.7 1.0

Reference:

S.Salar, N.E.Ball, H.Baaziz, J.C.Nix, R.C.Sobe, K.K.Compton, I.B.Zhulin, A.M.Brown, B.E.Scharf, F.D.Schubot. The Structural Analysis of the Periplasmic Domain of Sinorhizobium Meliloti Chemoreceptor Mcpz Reveals A Novel Fold and Suggests A Complex Mechanism of Transmembrane Signaling. Proteins 2023.
ISSN: ESSN 1097-0134
PubMed: 37213073
DOI: 10.1002/PROT.26510
Page generated: Fri Jul 28 04:52:15 2023

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