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Calcium in PDB 4gc7: Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt

Enzymatic activity of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt

All present enzymatic activity of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt:
2.7.7.7;

Protein crystallography data

The structure of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt, PDB code: 4gc7 was solved by R.L.Eoff, A.Ketkar, S.Banerjee, M.K.Zafar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.48 / 2.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 52.717, 101.085, 99.986, 90.00, 92.59, 90.00
R / Rfree (%) 20.6 / 26.5

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt (pdb code 4gc7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 9 binding sites of Calcium where determined in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt, PDB code: 4gc7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Calcium binding site 1 out of 9 in 4gc7

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Calcium binding site 1 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca402

b:87.9
occ:1.00
 OAS A:0OJ401 2.6 82.8 1.0
OD2 A:ASP7 2.6 70.2 1.0
OE1 A:GLU106 2.8 61.8 1.0
OAD A:0OJ401 2.9 68.5 1.0
PBE A:0OJ401 3.3 85.3 1.0
CA A:CA403 3.6 70.2 1.0
OAR A:0OJ401 3.6 72.2 1.0
CG A:ASP7 3.7 65.6 1.0
OD2 A:ASP105 3.7 62.3 1.0
OD1 A:ASP105 3.7 65.2 1.0
CAL A:0OJ401 3.7 69.5 1.0
O5' C:DC14 4.0 75.1 1.0
NZ A:LYS159 4.0 60.8 1.0
CD A:GLU106 4.0 64.3 1.0
C3' C:DC14 4.0 67.0 1.0
OD1 A:ASP7 4.1 68.2 1.0
C2' C:DC14 4.1 69.0 1.0
CG A:ASP105 4.1 62.4 1.0
OAT A:0OJ401 4.3 73.8 1.0
OAI A:0OJ401 4.5 88.0 1.0
PBD A:0OJ401 4.6 69.5 1.0
C5' C:DC14 4.7 71.0 1.0
CG A:GLU106 4.7 60.3 1.0
CAY A:0OJ401 4.9 69.3 1.0
OE2 A:GLU106 4.9 64.7 1.0
CB A:ASP7 4.9 61.2 1.0
O3' C:DC14 5.0 68.7 1.0

Calcium binding site 2 out of 9 in 4gc7

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Calcium binding site 2 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca403

b:70.2
occ:1.00
 OAS A:0OJ401 2.4 82.8 1.0
OD1 A:ASP7 2.7 68.2 1.0
OD2 A:ASP105 2.7 62.3 1.0
O A:PHE8 2.7 59.5 1.0
OAT A:0OJ401 2.8 73.8 1.0
OAR A:0OJ401 3.1 72.2 1.0
PBE A:0OJ401 3.1 85.3 1.0
OD2 A:ASP7 3.2 70.2 1.0
CG A:ASP7 3.3 65.6 1.0
PBD A:0OJ401 3.4 69.5 1.0
CA A:CA402 3.6 87.9 1.0
N A:TYR10 3.6 59.6 1.0
OAH A:0OJ401 3.7 61.0 1.0
CG A:ASP105 3.8 62.4 1.0
C A:PHE8 3.8 56.9 1.0
O A:HOH512 3.8 59.8 1.0
O A:HOH513 4.0 68.7 1.0
OAD A:0OJ401 4.0 68.5 1.0
CA A:ASP9 4.1 61.9 1.0
C A:ASP9 4.2 59.3 1.0
OAI A:0OJ401 4.3 88.0 1.0
CAL A:0OJ401 4.3 69.5 1.0
N A:PHE11 4.4 57.2 1.0
N A:ASP9 4.4 53.9 1.0
OD1 A:ASP105 4.5 65.2 1.0
CA A:TYR10 4.5 59.7 1.0
N A:PHE8 4.6 58.1 1.0
CB A:ASP105 4.7 60.6 1.0
CB A:ASP7 4.7 61.2 1.0
C A:ASP7 4.8 65.7 1.0
OAC A:0OJ401 4.8 78.7 1.0
CA A:PHE8 4.8 57.8 1.0
CB A:PHE11 4.9 57.7 1.0

Calcium binding site 3 out of 9 in 4gc7

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Calcium binding site 3 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca404

b:83.7
occ:1.00
 O A:HOH505 2.8 55.3 1.0
O A:ILE186 2.8 64.3 1.0
O A:ALA181 2.9 79.7 1.0
C A:ILE186 3.8 68.4 1.0
C A:ALA181 3.9 70.7 1.0
OP1 C:DC13 4.0 65.9 1.0
OP2 C:DC13 4.2 60.0 1.0
O A:VAL183 4.2 61.2 1.0
CA A:GLY187 4.4 65.1 1.0
N A:GLY187 4.4 67.9 1.0
CA A:ASP182 4.5 73.1 1.0
P C:DC13 4.5 63.6 1.0
N A:ASP182 4.7 68.3 1.0
CA A:ILE186 4.8 65.0 1.0
N A:ILE186 4.8 71.3 1.0
C A:ASP182 4.8 64.8 1.0
CA A:ALA181 4.8 73.0 1.0
C A:VAL183 5.0 66.7 1.0

Calcium binding site 4 out of 9 in 4gc7

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Calcium binding site 4 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca405

b:80.4
occ:1.00
 O C:HOH102 2.8 49.3 1.0
OD2 A:ASP294 2.9 60.6 1.0
OP2 C:DA10 3.1 61.6 1.0
O A:ILE295 3.3 59.1 1.0
OE2 B:GLU327 3.3 85.7 1.0
OD1 A:ASP294 3.4 66.6 1.0
O B:HOH521 3.4 69.4 1.0
CG A:ASP294 3.5 68.1 1.0
C3' C:DG9 3.7 64.9 1.0
OP1 C:DG9 3.7 66.0 1.0
O5' C:DG9 3.8 70.8 1.0
O C:HOH105 3.9 63.4 1.0
O3' C:DG9 4.0 71.6 1.0
P C:DA10 4.1 68.2 1.0
C5' C:DG9 4.1 60.9 1.0
CD B:GLU327 4.2 89.3 1.0
P C:DG9 4.3 64.8 1.0
CG2 A:VAL296 4.4 60.5 1.0
NH2 A:ARG328 4.4 64.5 1.0
C A:ILE295 4.4 55.8 1.0
C4' C:DG9 4.5 61.6 1.0
C2' C:DG9 4.7 60.2 1.0
CG B:GLU327 4.8 87.4 1.0
CB A:ASP294 4.9 65.0 1.0
CB B:GLU327 4.9 80.9 1.0
OP1 C:DA10 4.9 65.6 1.0
CA A:VAL296 5.0 56.0 1.0
OP2 C:DG9 5.0 56.5 1.0

Calcium binding site 5 out of 9 in 4gc7

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Calcium binding site 5 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca406

b:75.5
occ:1.00
 O A:HOH501 2.8 58.8 1.0
O A:GLU324 2.9 73.5 1.0
OE1 B:GLU325 3.1 77.5 1.0
OP1 E:DG8 3.3 55.2 1.0
CD B:GLU325 3.9 74.9 1.0
OE2 B:GLU325 3.9 71.8 1.0
C5' E:DG8 4.0 62.4 1.0
CE B:LYS321 4.0 68.2 1.0
NE B:ARG298 4.1 67.2 1.0
C A:GLU324 4.1 70.2 1.0
P E:DG8 4.4 54.0 1.0
CZ B:ARG298 4.5 64.7 1.0
OE2 A:GLU327 4.5 63.3 1.0
CD B:ARG298 4.5 61.5 1.0
O5' E:DG8 4.6 57.0 1.0
NZ B:LYS321 4.6 62.5 1.0
NH2 B:ARG298 4.6 64.8 1.0
CA A:GLU324 4.9 69.0 1.0

Calcium binding site 6 out of 9 in 4gc7

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Calcium binding site 6 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca402

b:64.5
occ:1.00
 OD2 B:ASP105 1.8 66.5 1.0
O B:HOH515 2.0 65.2 1.0
OD1 B:ASP7 2.0 66.3 1.0
OAI B:0OJ401 2.2 76.8 1.0
O B:PHE8 2.9 64.0 1.0
CG B:ASP105 2.9 64.3 1.0
CG B:ASP7 3.1 63.9 1.0
OAT B:0OJ401 3.2 66.5 1.0
PBE B:0OJ401 3.2 79.7 1.0
O B:HOH502 3.3 65.0 1.0
OD2 B:ASP7 3.4 65.8 1.0
OAR B:0OJ401 3.6 62.9 1.0
CB B:ASP105 3.6 55.5 1.0
CAL B:0OJ401 3.6 66.1 1.0
PBD B:0OJ401 3.7 70.4 1.0
CA B:CA405 3.7 88.1 1.0
OAH B:0OJ401 3.8 60.9 1.0
C B:PHE8 3.8 59.0 1.0
OD1 B:ASP105 3.9 75.7 1.0
OAD B:0OJ401 4.2 71.7 1.0
OAS B:0OJ401 4.3 59.7 1.0
N B:PHE8 4.3 52.1 1.0
CB B:ASP7 4.4 55.2 1.0
C B:ASP7 4.4 57.8 1.0
O B:ASP105 4.4 55.6 1.0
N B:TYR10 4.5 57.1 1.0
CA B:PHE8 4.6 56.5 1.0
N B:ASP9 4.7 52.9 1.0
CA B:ASP9 4.7 56.7 1.0
CA B:ASP7 4.8 55.3 1.0
O B:ASP7 4.8 58.5 1.0
N B:PHE11 4.8 57.5 1.0
CB B:PHE11 4.9 54.1 1.0
CA B:ASP105 4.9 56.3 1.0
C B:ASP9 4.9 58.4 1.0
CB B:PHE8 5.0 49.6 1.0
CAY B:0OJ401 5.0 68.0 1.0

Calcium binding site 7 out of 9 in 4gc7

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Calcium binding site 7 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca403

b:82.2
occ:1.00
 OD2 B:ASP294 2.8 62.4 1.0
OP2 E:DA10 3.1 54.6 1.0
OD1 B:ASP294 3.2 54.0 1.0
CG B:ASP294 3.4 59.0 1.0
P E:DA10 3.8 70.2 1.0
O3' E:DG9 3.9 64.0 1.0
OP1 E:DA10 4.1 54.0 1.0
C3' E:DG9 4.3 60.9 1.0
NH2 B:ARG328 4.8 64.5 1.0
C5' E:DG9 4.8 54.8 1.0
CB B:ASP294 4.9 51.2 1.0

Calcium binding site 8 out of 9 in 4gc7

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Calcium binding site 8 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca404

b:85.4
occ:1.00
 O B:ALA181 2.8 65.7 1.0
O B:ILE186 3.2 57.4 1.0
C B:ALA181 4.0 70.2 1.0
C B:ILE186 4.4 61.6 1.0
OP2 E:DC13 4.6 53.0 1.0
CA B:ASP182 4.6 71.3 1.0
OP1 E:DC13 4.6 65.0 1.0
O B:VAL183 4.7 64.8 1.0
N B:ASP182 4.7 69.7 1.0
C B:ASP182 4.8 63.9 1.0

Calcium binding site 9 out of 9 in 4gc7

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Calcium binding site 9 out of 9 in the Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of DPO4 in Complex with S-Mc-Dadp Opposite Dt within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca405

b:88.1
occ:1.00
 OD2 B:ASP7 2.9 65.8 1.0
OAI B:0OJ401 2.9 76.8 1.0
C5' E:DC14 3.0 79.1 1.0
OD2 B:ASP105 3.0 66.5 1.0
OE1 B:GLU106 3.1 72.0 1.0
OAS B:0OJ401 3.3 59.7 1.0
OD1 B:ASP105 3.4 75.7 1.0
OAR B:0OJ401 3.5 62.9 1.0
CAL B:0OJ401 3.6 66.1 1.0
CG B:ASP105 3.7 64.3 1.0
PBE B:0OJ401 3.7 79.7 1.0
CA B:CA402 3.7 64.5 1.0
CG B:ASP7 3.8 63.9 1.0
CD B:GLU106 3.9 67.9 1.0
O5' E:DC14 4.0 86.5 1.0
C4' E:DC14 4.0 76.7 0.7
OD1 B:ASP7 4.1 66.3 1.0
C3' E:DC14 4.1 73.5 0.7
OP1 E:DC14 4.3 81.4 1.0
CG B:GLU106 4.4 60.4 1.0
OAT B:0OJ401 4.6 66.5 1.0
PBD B:0OJ401 4.7 70.4 1.0
NZ B:LYS159 4.7 67.8 1.0
OE2 B:GLU106 4.8 72.2 1.0
P E:DC14 4.9 90.4 1.0
CAY B:0OJ401 4.9 68.0 1.0
OAD B:0OJ401 4.9 71.7 1.0

Reference:

A.Ketkar, M.K.Zafar, S.Banerjee, V.E.Marquez, M.Egli, R.L.Eoff. Differential Furanose Selection in the Active Sites of Archaeal Dna Polymerases Probed By Fixed-Conformation Nucleotide Analogues. Biochemistry V. 51 9234 2012.
ISSN: ISSN 0006-2960
PubMed: 23050956
DOI: 10.1021/BI301043K
Page generated: Sun Jul 14 07:04:37 2024

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