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Cobalt in PDB 6x8z: Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296)

Protein crystallography data

The structure of Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296), PDB code: 6x8z was solved by R.Mascarenhas, Z.Li, M.Koutmos, R.Banerjee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.64 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 103.222, 69.776, 64.266, 90.00, 101.15, 90.00
R / Rfree (%) 24.9 / 27.9

Cobalt Binding Sites:

The binding sites of Cobalt atom in the Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296) (pdb code 6x8z). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296), PDB code: 6x8z:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in 6x8z

Go back to Cobalt Binding Sites List in 6x8z
Cobalt binding site 1 out of 2 in the Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Co301

b:0.4
occ:0.93
CO A:B12301 0.0 0.4 0.9
N22 A:B12301 1.9 0.7 0.9
N21 A:B12301 1.9 0.7 0.9
N23 A:B12301 1.9 0.2 0.9
N24 A:B12301 1.9 0.2 0.9
SG A:CYS261 2.3 0.5 1.0
C19 A:B12301 2.8 0.3 0.9
C9 A:B12301 2.9 0.6 0.9
C1 A:B12301 2.9 0.4 0.9
C4 A:B12301 2.9 0.6 0.9
C6 A:B12301 2.9 0.8 0.9
C11 A:B12301 2.9 0.6 0.9
C14 A:B12301 3.0 0.2 0.9
C16 A:B12301 3.0 0.2 0.9
C10 A:B12301 3.2 0.8 0.9
H202 A:B12301 3.2 0.4 0.9
H201 A:B12301 3.3 0.4 0.9
C5 A:B12301 3.3 0.2 0.9
C20 A:B12301 3.3 0.8 0.9
C15 A:B12301 3.3 0.8 0.9
H91 A:B12301 3.4 0.8 0.9
CB A:CYS261 3.7 97.9 1.0
HB3 A:CYS261 3.7 0.9 1.0
H471 A:B12301 3.9 0.6 0.9
HB2 A:CYS261 3.9 0.9 1.0
H371 A:B12301 4.0 0.4 0.9
C3 A:B12301 4.0 0.2 0.9
C7 A:B12301 4.1 0.6 0.9
H10 A:B12301 4.1 0.8 0.9
C8 A:B12301 4.1 0.0 0.9
C12 A:B12301 4.1 0.5 0.9
C2 A:B12301 4.1 0.2 0.9
C18 A:B12301 4.2 0.3 0.9
H3 A:B12301 4.2 0.4 0.9
C13 A:B12301 4.2 0.6 0.9
H253 A:B12301 4.3 0.9 0.9
C17 A:B12301 4.3 0.3 0.9
H203 A:B12301 4.3 0.4 0.9
C47 A:B12301 4.5 0.5 0.9
C37 A:B12301 4.5 0.8 0.9
C35 A:B12301 4.6 0.6 0.9
H8 A:B12301 4.7 0.7 0.9
C53 A:B12301 4.7 0.5 0.9
H13 A:B12301 4.8 0.9 0.9
H472 A:B12301 4.8 0.6 0.9
C25 A:B12301 4.8 0.8 0.9
H351 A:B12301 4.8 0.6 0.9
H18 A:B12301 4.9 0.4 0.9
O39 A:B12301 4.9 0.6 0.9
H532 A:B12301 4.9 0.9 0.9
H552 A:B12301 4.9 0.1 0.9
H543 A:B12301 4.9 0.4 0.9
HA A:CYS261 5.0 0.9 1.0
CA A:CYS261 5.0 86.2 1.0

Cobalt binding site 2 out of 2 in 6x8z

Go back to Cobalt Binding Sites List in 6x8z
Cobalt binding site 2 out of 2 in the Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296)


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of N-Truncated Human B12 Chaperone Cbld(C262S)- Thiolato-Cob(III)Alamin Complex (108-296) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Co301

b:59.4
occ:1.00
CO B:B12301 0.0 59.4 1.0
N23 B:B12301 1.8 63.2 1.0
N21 B:B12301 1.9 68.8 1.0
N24 B:B12301 1.9 64.3 1.0
N22 B:B12301 1.9 66.8 1.0
SG B:CYS261 2.2 70.7 1.0
N3B B:B12301 2.5 65.8 1.0
C11 B:B12301 2.8 60.9 1.0
C9 B:B12301 2.8 66.1 1.0
C4 B:B12301 2.9 69.7 1.0
C14 B:B12301 2.9 60.0 1.0
C16 B:B12301 2.9 64.3 1.0
C1 B:B12301 2.9 68.8 1.0
C19 B:B12301 2.9 67.4 1.0
C6 B:B12301 2.9 70.1 1.0
C10 B:B12301 3.2 62.7 1.0
C5 B:B12301 3.3 69.7 1.0
H203 B:B12301 3.3 81.1 1.0
H91 B:B12301 3.3 81.4 1.0
C2B B:B12301 3.4 63.5 1.0
C15 B:B12301 3.4 61.8 1.0
CB B:CYS261 3.5 61.3 1.0
H2B B:B12301 3.5 76.6 1.0
C9B B:B12301 3.5 68.5 1.0
HB2 B:CYS261 3.5 74.0 1.0
C20 B:B12301 3.6 67.2 1.0
HB3 B:CYS261 3.6 74.0 1.0
H4B B:B12301 3.6 83.8 1.0
H202 B:B12301 3.9 81.1 1.0
H262 B:B12301 3.9 84.1 1.0
H372 B:B12301 3.9 88.8 1.0
C4B B:B12301 4.0 69.5 1.0
C18 B:B12301 4.1 67.8 1.0
H10 B:B12301 4.1 75.7 1.0
C2 B:B12301 4.1 70.0 1.0
C12 B:B12301 4.2 60.4 1.0
C3 B:B12301 4.2 70.6 1.0
C13 B:B12301 4.2 59.3 1.0
C7 B:B12301 4.2 70.3 1.0
C17 B:B12301 4.2 67.0 1.0
C8 B:B12301 4.2 70.2 1.0
H18 B:B12301 4.2 81.8 1.0
H543 B:B12301 4.3 80.7 1.0
H351 B:B12301 4.4 87.2 1.0
H482 B:B12301 4.4 68.7 1.0
H201 B:B12301 4.4 81.1 1.0
H461 B:B12301 4.5 72.3 1.0
H412 B:B12301 4.5 89.0 1.0
C35 B:B12301 4.5 72.3 1.0
C26 B:B12301 4.5 69.7 1.0
C37 B:B12301 4.6 73.6 1.0
N1B B:B12301 4.6 62.4 1.0
C54 B:B12301 4.7 66.9 1.0
C8B B:B12301 4.7 67.0 1.0
H542 B:B12301 4.8 80.7 1.0
H B:CYS261 4.8 76.6 1.0
H302 B:B12301 4.8 87.6 1.0
C46 B:B12301 4.8 59.9 1.0
H3 B:B12301 4.8 85.2 1.0
CA B:CYS261 4.8 61.3 1.0
H13 B:B12301 4.8 71.6 1.0
C53 B:B12301 4.9 61.1 1.0
H8 B:B12301 4.9 84.7 1.0
H261 B:B12301 4.9 84.1 1.0
C48 B:B12301 4.9 56.9 1.0
C41 B:B12301 4.9 73.8 1.0

Reference:

Z.Li, R.Mascarenhas, U.T.Twahir, A.Kallon, A.Deb, M.Yaw, J.Penner-Hahn, M.Koutmos, K.Warncke, R.Banerjee. An Interprotein Co-S Coordination Complex in the B 12 -Trafficking Pathway. J.Am.Chem.Soc. V. 142 16334 2020.
ISSN: ESSN 1520-5126
PubMed: 32871076
DOI: 10.1021/JACS.0C06590
Page generated: Sun Dec 13 10:54:00 2020

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