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Calcium in PDB 9kky: Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine

Enzymatic activity of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine

All present enzymatic activity of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine:
4.2.99.18;

Protein crystallography data

The structure of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine, PDB code: 9kky was solved by T.Imura, K.-C.Yang, Y.Hosokawa, H.-Y.Shih, Y.Ban, J.Yamamoto, M.Maestre-Reyna, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.35 / 2.81
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 89.673, 89.673, 211.766, 90, 90, 120
R / Rfree (%) 22.4 / 26.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine (pdb code 9kky). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine, PDB code: 9kky:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 9kky

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Calcium binding site 1 out of 4 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:93.6
occ:1.00
 OP1 C:DC26 2.2 80.6 1.0
O A:CYS241 2.3 65.7 1.0
O A:LEU243 2.5 65.9 1.0
O A:VAL246 2.6 63.9 1.0
P C:DC26 3.3 84.3 1.0
C A:CYS241 3.4 65.2 1.0
OP2 C:DC26 3.4 86.2 1.0
C A:LEU243 3.5 65.7 1.0
C A:VAL246 3.6 63.9 1.0
N A:VAL246 3.9 62.5 1.0
C A:ILE242 3.9 62.4 1.0
O A:ILE242 3.9 62.5 1.0
N A:LEU243 4.1 66.2 1.0
CA A:CYS241 4.1 65.0 1.0
CA A:VAL246 4.2 62.4 1.0
N A:PRO244 4.2 67.4 1.0
CA A:PRO244 4.3 67.4 1.0
N A:ILE242 4.3 62.7 1.0
O3' C:DT25 4.3 85.2 1.0
N A:GLY245 4.4 62.7 1.0
CA A:LEU243 4.4 65.8 1.0
CB A:VAL246 4.4 61.2 1.0
O5' C:DC26 4.4 90.9 1.0
CA A:ILE242 4.5 63.0 1.0
C A:PRO244 4.6 67.1 1.0
N A:GLY247 4.7 66.0 1.0
CB A:CYS241 4.8 66.2 1.0
O A:LEU240 4.9 63.4 1.0
C A:GLY245 5.0 63.0 1.0

Calcium binding site 2 out of 4 in 9kky

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Calcium binding site 2 out of 4 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:121.9
occ:1.00
 OD1 A:ASP61 3.2 92.7 1.0
OD2 A:ASP61 3.7 95.9 1.0
CG A:ASP61 3.9 94.1 1.0
OD2 A:ASP136 4.5 68.6 1.0
CG A:ASP136 4.5 68.4 1.0
OD1 A:ASP136 4.6 69.2 1.0
O A:HOH538 4.8 57.9 1.0

Calcium binding site 3 out of 4 in 9kky

Go back to Calcium Binding Sites List in 9kky
Calcium binding site 3 out of 4 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:109.1
occ:1.00
 NH2 A:ARG46 3.4 56.3 1.0
O A:HOH546 3.4 49.0 1.0
N A:HIS179 3.6 64.1 1.0
O A:THR177 3.9 64.5 1.0
CB A:HIS179 4.1 63.7 1.0
CD2 A:HIS179 4.2 63.4 1.0
O A:HIS179 4.2 63.6 1.0
CA A:HIS179 4.3 64.1 1.0
CB A:CYS163 4.4 59.2 1.0
CA A:TYR178 4.4 56.1 1.0
C A:TYR178 4.5 56.0 1.0
CG A:GLN164 4.5 71.5 1.0
CG A:HIS179 4.5 63.6 1.0
CZ A:ARG46 4.5 55.4 1.0
CG A:GLU160 4.6 71.1 1.0
O A:GLU160 4.6 68.7 1.0
C A:HIS179 4.8 64.0 1.0
NE2 A:GLN164 4.8 72.9 1.0
C A:THR177 4.9 64.7 1.0
NE A:ARG46 4.9 55.1 1.0

Calcium binding site 4 out of 4 in 9kky

Go back to Calcium Binding Sites List in 9kky
Calcium binding site 4 out of 4 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:96.6
occ:1.00
 OE1 A:GLU92 3.6 81.8 1.0
CG1 A:VAL77 3.6 55.7 1.0
OE2 A:GLU92 3.7 83.3 1.0
CB A:SER86 4.0 96.4 1.0
CB A:ARG79 4.1 98.8 1.0
O A:SER86 4.1 90.9 1.0
CD A:GLU92 4.1 82.2 1.0
O A:ARG87 4.6 91.7 1.0
C A:SER86 4.6 92.4 1.0
CA A:SER86 4.7 94.3 1.0
N A:SER86 4.7 93.7 1.0
OG A:SER86 4.8 98.8 1.0
N A:ARG79 4.9 95.0 1.0
O A:VAL77 4.9 56.6 1.0
CA A:ARG79 5.0 96.9 1.0

Reference:

T.Imura, Y.Hosokawa, K.C.Yang, Y.Ban, H.Y.Shih, J.Yamamoto, M.Maestre-Reyna. Revisiting the Co-Crystal Structure of A Dna Glycosylase with Photocaged Substrate: A Suitable Time-Resolved Crystallography Target? Iucrj 2025.
ISSN: ESSN 2052-2525
PubMed: 40658017
DOI: 10.1107/S2052252525006062
Page generated: Mon Aug 4 18:53:46 2025

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