Atomistry » Calcium » PDB 4fsd-4gg1 » 4gc7
Atomistry »
  Calcium »
    PDB 4fsd-4gg1 »
      4gc7 »

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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Go back to Calcium Binding Sites List in 4gc7
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

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy