Zinc in PDB 6wo0: Human Artemis/SNM1C Catalytic Domain, Crystal Form 1

Protein crystallography data

The structure of Human Artemis/SNM1C Catalytic Domain, Crystal Form 1, PDB code: 6wo0 was solved by F.Karim, S.Liu, A.R.Laciak, L.Volk, M.Rosenblum, R.Curtis, N.Huang, G.Carr, G.Zhu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.54 / 1.97
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.690, 111.010, 55.160, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 27

Zinc Binding Sites:

The binding sites of Zinc atom in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 1 (pdb code 6wo0). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 1, PDB code: 6wo0:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 6wo0

Go back to Zinc Binding Sites List in 6wo0
Zinc binding site 1 out of 2 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn401

b:43.6
occ:1.00
ND1 A:HIS228 1.9 44.8 1.0
ND1 A:HIS254 2.2 43.1 1.0
SG A:CYS256 2.3 44.5 1.0
SG A:CYS272 2.4 46.7 1.0
CE1 A:HIS228 2.6 49.3 1.0
CE1 A:HIS254 3.1 43.5 1.0
CG A:HIS228 3.2 47.0 1.0
CB A:CYS272 3.2 46.0 1.0
CG A:HIS254 3.2 43.4 1.0
CB A:CYS256 3.2 44.8 1.0
CB A:HIS254 3.5 42.9 1.0
CB A:HIS228 3.8 48.3 1.0
NE2 A:HIS228 3.8 47.5 1.0
CD2 A:HIS228 4.1 48.8 1.0
N A:CYS272 4.2 43.3 1.0
NE2 A:HIS254 4.2 45.2 1.0
CD2 A:HIS254 4.3 43.5 1.0
CA A:CYS272 4.3 45.9 1.0
CA A:HIS254 4.5 42.8 1.0
CA A:CYS256 4.5 44.0 1.0
N A:CYS256 4.6 44.0 1.0
CB A:LEU270 4.6 40.7 1.0
CG A:ARG249 4.7 58.0 1.0
CD1 A:LEU270 4.9 41.3 1.0
CD A:PRO271 5.0 43.1 1.0

Zinc binding site 2 out of 2 in 6wo0

Go back to Zinc Binding Sites List in 6wo0
Zinc binding site 2 out of 2 in the Human Artemis/SNM1C Catalytic Domain, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human Artemis/SNM1C Catalytic Domain, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:45.1
occ:1.00
O2 A:GOL403 1.9 37.0 1.0
NE2 A:HIS33 1.9 42.4 1.0
NE2 A:HIS115 2.2 39.3 1.0
O A:HOH503 2.2 43.2 1.0
OD2 A:ASP136 2.3 45.0 1.0
ND1 A:HIS35 2.3 45.6 1.0
CE1 A:HIS33 2.9 41.4 1.0
CE1 A:HIS115 3.0 39.5 1.0
CD2 A:HIS33 3.0 43.1 1.0
C2 A:GOL403 3.2 43.3 1.0
CD2 A:HIS115 3.2 41.4 1.0
CG A:ASP136 3.3 42.4 1.0
CG A:HIS35 3.3 46.2 1.0
CE1 A:HIS35 3.3 45.8 1.0
CB A:HIS35 3.5 47.0 1.0
CB A:ASP136 3.6 41.3 1.0
C1 A:GOL403 3.8 47.7 1.0
ND1 A:HIS33 4.0 41.9 1.0
CG A:HIS33 4.1 43.1 1.0
ND1 A:HIS115 4.2 40.7 1.0
C3 A:GOL403 4.2 45.2 1.0
CG A:HIS115 4.3 41.5 1.0
CE1 A:HIS38 4.3 46.9 1.0
ND1 A:HIS38 4.4 50.1 1.0
OD1 A:ASP136 4.4 44.7 1.0
NE2 A:HIS35 4.4 46.1 1.0
CD2 A:HIS35 4.4 46.2 1.0
CE1 A:HIS319 4.6 41.1 1.0
O A:HOH532 4.9 61.8 1.0

Reference:

M.F.Karim, S.Liu, A.R.Laciak, L.Volk, M.Koszelak-Rosenblum, M.R.Lieber, M.Wu, R.Curtis, N.N.Huang, G.Carr, G.Zhu. Structural Analysis of the Catalytic Domain of Artemis Endonuclease/SNM1C Reveals Distinct Structural Features. J.Biol.Chem. V. 295 12368 2020.
ISSN: ESSN 1083-351X
PubMed: 32576658
DOI: 10.1074/JBC.RA120.014136
Page generated: Wed Dec 16 13:05:53 2020

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