Ytterbium in PDB 5npl: Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution

The structure of Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution, PDB code: 5npl was solved by C.Hackenberg, J.Hakanpaa, S.V.Antonyuk, E.Dittmann, V.S.Lamzin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.79
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	79.890, 120.734, 117.548, 90.00, 90.00, 90.00
R / Rfree (%)	18.6 / 21.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Ytterbium atom in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution (pdb code 5npl). This binding sites where shown within 5.0 Angstroms radius around Ytterbium atom.
In total 17 binding sites of Ytterbium where determined in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution, PDB code: 5npl:
Jump to Ytterbium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Ytterbium binding site 1 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb301 b:49.9 occ:1.00 O1 A:DO3302 2.1 56.5 1.0 O4 A:DO3302 2.2 61.8 1.0 O5 A:DO3302 2.4 72.3 1.0 N4 A:DO3302 2.4 67.4 1.0 O7 A:DO3302 2.5 60.7 1.0 C2 A:DO3302 3.1 64.4 1.0 C9 A:DO3302 3.1 63.3 1.0 C16 A:DO3302 3.2 65.9 1.0 C11 A:DO3302 3.2 68.7 1.0 C13 A:DO3302 3.2 73.4 1.0 C14 A:DO3302 3.2 70.1 1.0 C6 A:DO3302 3.3 65.9 1.0 C7 A:DO3302 3.3 64.7 1.0 C15 A:DO3302 3.3 63.2 1.0 N3 A:DO3302 3.4 67.4 1.0 N2 A:DO3302 3.4 65.6 1.0 C5 A:DO3302 3.5 63.1 1.0 C12 A:DO3302 3.6 68.5 1.0 C1 A:DO3302 3.6 65.2 1.0 N1 A:DO3302 3.6 67.3 1.0 C3 A:DO3302 3.7 66.0 1.0 C4 A:DO3302 3.7 65.6 1.0 C8 A:DO3302 3.8 65.8 1.0 C10 A:DO3302 3.9 64.6 1.0 O2 A:DO3302 4.0 64.6 1.0 C17 A:DO3302 4.2 66.6 1.0 O3 A:DO3302 4.3 64.6 1.0 O6 A:DO3302 4.4 74.6 1.0

Ytterbium binding site 2 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


Mono view


Stereo pair view

A full contact list of Ytterbium with other atoms in the Yb binding site number 2 of Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb303 b:39.3 occ:0.63 O1 A:DO3304 2.1 46.7 0.6 N4 A:DO3304 2.4 53.3 0.6 O4 A:DO3304 2.6 56.6 0.6 C5 A:DO3304 2.9 56.5 0.6 O5 A:DO3304 2.9 61.6 0.6 C6 A:DO3304 2.9 54.6 0.6 C2 A:DO3304 3.0 54.2 0.6 C9 A:DO3304 3.1 50.7 0.6 C16 A:DO3304 3.2 48.8 0.6 C3 A:DO3304 3.2 57.7 0.6 O7 A:DO3304 3.3 43.2 0.6 C1 A:DO3304 3.3 52.6 0.6 N2 A:DO3304 3.3 56.0 0.6 C17 A:DO3304 3.4 46.2 0.6 N3 A:DO3304 3.4 60.2 0.6 C7 A:DO3304 3.4 53.4 0.6 C15 A:DO3304 3.4 45.3 0.6 N1 A:DO3304 3.4 52.7 0.6 C11 A:DO3304 3.5 55.7 0.6 C4 A:DO3304 3.5 58.5 0.6 C10 A:DO3304 3.5 52.4 0.6 C8 A:DO3304 3.6 52.9 0.6 C13 A:DO3304 3.7 60.7 0.6 C12 A:DO3304 3.8 56.1 0.6 C14 A:DO3304 4.0 61.5 0.6 O2 A:DO3304 4.2 48.0 0.6 O3 A:DO3304 4.5 54.1 0.6 O6 A:DO3304 4.7 60.0 0.6

Ytterbium binding site 3 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb305 b:48.2 occ:0.51 OE2 A:GLU42 3.1 76.2 1.0 CD A:GLU42 4.0 67.0 1.0 OE1 A:GLU42 4.0 72.0 1.0 NH1 A:ARG19 5.0 0.9 1.0

Ytterbium binding site 4 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ A:Yb306 b:48.9 occ:0.36 NH2 A:ARG37 3.4 61.4 1.0 CZ A:ARG37 4.6 60.4 1.0 NH1 A:ARG37 4.9 63.8 1.0

Ytterbium binding site 5 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range:

Ytterbium binding site 6 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range:

Ytterbium binding site 7 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range:

Ytterbium binding site 8 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range: probe atom residue distance (Å) B Occ B:Yb302 b:59.7 occ:0.34 NH2 B:ARG37 3.6 66.8 1.0 CZ B:ARG37 4.7 68.1 1.0 NH1 B:ARG37 4.9 70.1 1.0

Ytterbium binding site 9 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range:

Ytterbium binding site 10 out of 17 in the Crystal Structure of Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution


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 Hexameric Cbs-CP12 Protein From Bloom-Forming Cyanobacteria, Yb-Derivative at 2.8 A Resolution within 5.0Å range:

C.Hackenberg, J.Hakanpaa, F.Cai, S.Antonyuk, C.Eigner, S.Meissner, M.Laitaoja, J.Janis, C.A.Kerfeld, E.Dittmann, V.S.Lamzin. Structural and Functional Insights Into the Unique Cbs-CP12 Fusion Protein Family in Cyanobacteria. Proc. Natl. Acad. Sci. V. 115 7141 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 29915055
DOI: 10.1073/PNAS.1806668115