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Calcium in PDB 9kl8: Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection

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

All present enzymatic activity of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection:
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 After Deprotection, PDB code: 9kl8 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) 42.01 / 2.48
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 91.46, 91.46, 212.77, 90, 90, 120
R / Rfree (%) 21.3 / 25.1

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 After Deprotection (pdb code 9kl8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection, PDB code: 9kl8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 9kl8

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Calcium binding site 1 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


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 After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:120.4
occ:1.00
 C5' C:DA22 3.6 153.1 1.0
N3 C:DA22 3.8 134.6 1.0
C2 C:DA22 4.0 142.7 1.0
O5' C:DA22 4.2 143.0 1.0
C4' C:DA22 4.6 149.1 1.0
C3' C:DA22 4.8 144.2 1.0
C2' C:DA22 4.9 125.2 1.0

Calcium binding site 2 out of 9 in 9kl8

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Calcium binding site 2 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


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 After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca401

b:85.3
occ:1.00
 O A:CYS241 2.4 60.1 1.0
O A:LEU243 2.5 55.0 1.0
OP1 C:DC26 2.5 76.1 1.0
O A:VAL246 2.8 55.6 1.0
OP2 C:DC26 3.3 78.4 1.0
P C:DC26 3.4 76.4 1.0
C A:CYS241 3.4 59.7 1.0
C A:LEU243 3.6 53.9 1.0
C A:VAL246 3.8 48.6 1.0
C A:ILE242 4.0 55.4 1.0
O A:ILE242 4.0 58.0 1.0
N A:VAL246 4.1 59.6 1.0
CA A:CYS241 4.1 55.7 1.0
N A:LEU243 4.1 48.0 1.0
N A:ILE242 4.3 55.4 1.0
CA A:PRO244 4.4 49.3 1.0
O3' C:DT25 4.4 59.1 1.0
N A:PRO244 4.4 53.7 1.0
CA A:VAL246 4.4 50.9 1.0
CA A:ILE242 4.5 58.8 1.0
N A:GLY245 4.5 60.1 1.0
CA A:LEU243 4.5 48.9 1.0
O5' C:DC26 4.6 78.8 1.0
CB A:VAL246 4.7 49.7 1.0
CB A:CYS241 4.7 59.4 1.0
C A:PRO244 4.8 55.2 1.0
N A:GLY247 4.9 55.8 1.0
O A:LEU240 5.0 56.5 1.0

Calcium binding site 3 out of 9 in 9kl8

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Calcium binding site 3 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


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 After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:130.6
occ:1.00
 OD1 A:ASP61 3.0 94.0 1.0
OD2 A:ASP61 3.6 97.7 1.0
CG A:ASP61 3.7 85.8 1.0

Calcium binding site 4 out of 9 in 9kl8

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Calcium binding site 4 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


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 After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:83.3
occ:1.00
 NH2 A:ARG46 3.1 47.6 1.0
N A:HIS179 3.4 50.9 1.0
CB A:HIS179 3.7 51.0 1.0
O A:HOH544 3.8 53.3 1.0
O A:THR177 3.8 50.0 1.0
CA A:HIS179 4.0 45.8 1.0
O A:HIS179 4.0 50.1 1.0
CD2 A:HIS179 4.0 47.8 1.0
CG A:HIS179 4.2 58.9 1.0
O A:HOH508 4.2 62.8 1.0
C A:TYR178 4.2 48.3 1.0
CA A:TYR178 4.3 47.7 1.0
CZ A:ARG46 4.4 47.7 1.0
CB A:CYS163 4.4 46.3 1.0
C A:HIS179 4.5 47.1 1.0
CG A:GLN164 4.7 71.0 1.0
O A:GLU160 4.8 51.6 1.0
CG A:GLU160 4.8 64.4 1.0
C A:THR177 4.8 40.3 1.0
NE2 A:GLN164 4.9 69.6 1.0
NE A:ARG46 5.0 50.1 1.0
N A:GLN164 5.0 52.1 1.0

Calcium binding site 5 out of 9 in 9kl8

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Calcium binding site 5 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:112.7
occ:1.00
 OD1 A:ASP268 3.5 92.4 1.0
O4' C:8OG23 3.6 148.8 1.0
ND1 A:HIS270 3.7 76.9 1.0
CE2 A:PHE319 3.7 73.4 1.0
N3 C:8OG23 3.8 120.2 0.7
C1' C:8OG23 4.1 133.8 1.0
CB A:HIS270 4.2 69.5 1.0
C4 C:8OG23 4.2 118.1 0.7
CZ A:PHE319 4.2 74.7 1.0
CD2 A:PHE319 4.2 70.7 1.0
N9 C:8OG23 4.3 119.4 0.7
CG A:HIS270 4.4 81.5 1.0
CG A:ASP268 4.4 80.6 1.0
C2 C:8OG23 4.4 118.0 0.7
OD2 A:ASP268 4.6 78.2 1.0
C4' C:8OG23 4.6 146.3 1.0
N2 C:8OG23 4.8 119.5 0.7
CE1 A:HIS270 4.8 71.0 1.0
OP2 C:8OG23 4.8 200.1 1.0
CE1 A:PHE319 5.0 73.4 1.0

Calcium binding site 6 out of 9 in 9kl8

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Calcium binding site 6 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca407

b:114.1
occ:0.50
 O A:ASP278 3.7 69.3 1.0
O A:HOH521 4.2 62.2 1.0
C A:ASP278 4.4 75.6 1.0
CA A:ASP278 4.7 66.8 1.0

Calcium binding site 7 out of 9 in 9kl8

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Calcium binding site 7 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca408

b:92.3
occ:1.00
 OH A:TYR233 3.8 64.6 1.0
CE2 A:TYR233 4.0 57.8 1.0
CZ A:TYR233 4.1 61.3 1.0
CG A:HIS237 4.5 60.6 1.0
ND1 A:HIS237 4.5 55.6 1.0
CD2 A:HIS237 4.6 62.6 1.0
CE1 A:HIS237 4.7 60.9 1.0
NE2 A:HIS237 4.7 69.8 1.0
NH2 A:ARG304 4.8 52.5 1.0
CD2 A:TYR233 4.9 46.5 1.0
CB A:HIS237 4.9 55.4 1.0
CE1 A:TYR233 4.9 49.0 1.0
OD1 A:ASP252 5.0 56.4 1.0

Calcium binding site 8 out of 9 in 9kl8

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Calcium binding site 8 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca409

b:106.2
occ:1.00
 OG1 A:THR248 3.5 61.5 1.0
SG A:CYS241 3.6 71.5 1.0
NE2 A:HIS237 4.2 69.8 1.0
CB A:CYS241 4.3 59.4 1.0
CD2 A:HIS237 4.5 62.6 1.0
CB A:THR248 4.8 57.1 1.0

Calcium binding site 9 out of 9 in 9kl8

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Calcium binding site 9 out of 9 in the Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Co-Crystal Structure of Human 8-Oxoguanine Glycosylase N149C Mutant with Dna Containing Photocaged 8-Oxoguanine After Deprotection within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca410

b:111.0
occ:1.00
 CG A:PRO27 4.6 70.6 1.0
CD A:PRO27 4.7 66.2 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 18:53:47 2025

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