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Sodium in PDB 3v7j: Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex

Enzymatic activity of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex

All present enzymatic activity of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex:
2.7.7.7;

Protein crystallography data

The structure of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex, PDB code: 3v7j was solved by S.Rangarajan, J.Jaeger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 17.02 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.779, 77.114, 116.653, 90.00, 90.00, 90.00
R / Rfree (%) 21.1 / 24.3

Other elements in 3v7j:

The structure of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex (pdb code 3v7j). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex, PDB code: 3v7j:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 3v7j

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Sodium binding site 1 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na336

b:22.2
occ:1.00
 O A:HOH491 3.0 22.2 1.0
O A:HOH610 3.2 26.3 1.0
OD1 A:ASP190 3.3 27.0 1.0
O A:HOH426 3.3 6.6 1.0
O A:ASP190 3.4 20.2 1.0
O A:CYS178 3.8 13.5 1.0
CA A:GLY179 3.9 22.7 1.0
N A:ASP192 4.0 15.4 1.0
O A:HOH488 4.0 22.2 1.0
CB A:ASP192 4.1 25.8 1.0
C A:ASP190 4.1 18.9 1.0
CA A:MET191 4.3 17.3 1.0
C A:CYS178 4.4 12.8 1.0
N A:GLY179 4.4 21.9 1.0
O A:HOH502 4.5 22.2 1.0
CG A:ASP190 4.5 27.0 1.0
N A:MET191 4.5 17.1 1.0
C A:MET191 4.5 16.9 1.0
C A:GLY179 4.6 24.5 1.0
N A:SER180 4.7 25.4 1.0
CA A:ASP192 4.7 14.7 1.0
N A:ASP190 4.9 20.6 1.0
CE A:MET155 4.9 19.4 1.0
OG A:SER188 4.9 23.6 1.0
O A:HOH469 5.0 22.8 1.0
CA A:ASP190 5.0 19.2 1.0

Sodium binding site 2 out of 8 in 3v7j

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Sodium binding site 2 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na337

b:30.7
occ:1.00
 OD1 A:ASP130 3.4 22.3 1.0
O A:HOH464 3.4 22.8 1.0
O A:LYS127 3.9 13.6 1.0
CG A:ASP130 4.1 21.6 1.0
OD2 A:ASP130 4.4 21.3 1.0
OD1 A:ASN128 4.7 21.0 1.0

Sodium binding site 3 out of 8 in 3v7j

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Sodium binding site 3 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na338

b:13.8
occ:1.00
 OP1 P:DG6 3.6 14.8 1.0
CA A:THR104 3.6 7.1 1.0
O A:ARG102 3.6 13.6 1.0
O A:HOH434 3.7 9.5 1.0
O A:THR101 3.7 6.9 1.0
N A:THR104 3.7 7.2 1.0
C A:VAL103 3.9 7.2 1.0
C A:ARG102 3.9 13.5 1.0
O A:VAL103 3.9 7.1 1.0
CB A:THR104 4.2 7.2 1.0
CA A:ARG102 4.4 13.4 1.0
N A:VAL103 4.5 7.4 1.0
OG1 A:THR104 4.6 7.1 1.0
P P:DG6 4.6 14.6 1.0
C A:THR101 4.7 7.0 1.0
CA A:VAL103 4.7 7.5 1.0
O A:HOH552 4.8 23.1 1.0
C A:THR104 4.8 7.1 1.0
OP2 P:DG6 4.9 15.8 1.0
O A:ILE106 4.9 6.8 1.0
O P:HOH218 4.9 23.1 1.0
N A:GLY105 5.0 7.0 1.0

Sodium binding site 4 out of 8 in 3v7j

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Sodium binding site 4 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na339

b:35.8
occ:1.00
 O A:HOH599 3.8 26.3 1.0
O A:HOH516 4.4 23.1 1.0
O A:HOH372 4.8 7.5 1.0

Sodium binding site 5 out of 8 in 3v7j

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Sodium binding site 5 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na340

b:27.4
occ:1.00
 OH A:TYR39 3.1 7.5 1.0
NZ A:LYS72 3.2 7.5 1.0
CB A:LYS68 3.5 33.8 1.0
CE A:LYS72 3.7 7.2 1.0
CD A:LYS68 3.9 35.0 1.0
O A:HOH397 4.0 11.7 1.0
O A:HOH404 4.2 3.4 1.0
CG A:LYS68 4.2 34.3 1.0
CZ A:TYR39 4.3 7.3 1.0
CD A:LYS72 4.5 7.1 1.0
C A:LYS68 4.5 7.7 1.0
O A:LYS68 4.6 7.7 1.0
CA A:LYS68 4.6 8.1 1.0
CE1 A:TYR39 4.8 7.3 1.0
CE A:LYS68 5.0 35.6 1.0

Sodium binding site 6 out of 8 in 3v7j

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Sodium binding site 6 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na341

b:38.6
occ:1.00
 O A:HOH512 3.6 23.1 1.0
CA A:ALA38 3.9 9.7 1.0
O A:HOH406 3.9 5.6 1.0
N A:ALA38 4.1 9.6 1.0
CD A:LYS41 4.3 31.4 1.0
CB A:ALA38 4.3 7.3 1.0
C A:ASN37 4.6 8.0 1.0
NZ A:LYS41 4.6 32.0 1.0
O A:ASN37 4.7 8.1 1.0
O A:HIS34 4.8 9.8 1.0
CE A:LYS41 5.0 31.7 1.0

Sodium binding site 7 out of 8 in 3v7j

Go back to Sodium Binding Sites List in 3v7j
Sodium binding site 7 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na342

b:23.3
occ:1.00
 O A:ASN28 3.3 31.8 1.0
O A:PRO108 3.3 10.5 1.0
O A:VAL29 3.3 14.6 1.0
OE1 A:GLN31 3.4 16.0 1.0
CB A:ARG112 3.7 38.4 1.0
CA A:VAL29 3.8 14.0 1.0
CG A:GLN31 3.9 16.5 1.0
C A:VAL29 3.9 13.8 1.0
CD A:GLN31 3.9 16.4 1.0
CD A:ARG112 3.9 40.6 1.0
C A:ASN28 4.0 30.5 1.0
CD1 A:ILE97 4.0 7.9 1.0
C A:PRO108 4.0 10.3 1.0
CB A:PRO108 4.2 6.6 1.0
N A:VAL29 4.2 13.7 1.0
N A:ARG112 4.2 15.7 1.0
CA A:ARG112 4.3 16.1 1.0
CG2 A:ILE97 4.3 7.3 1.0
CA A:PRO108 4.3 10.2 1.0
CG A:ARG112 4.4 39.6 1.0
NH1 A:ARG112 4.5 40.6 1.0
O A:SER30 4.6 33.3 1.0
CG1 A:ILE97 4.8 8.0 1.0
NE A:ARG112 5.0 41.3 1.0
N A:SER109 5.0 9.8 1.0

Sodium binding site 8 out of 8 in 3v7j

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Sodium binding site 8 out of 8 in the Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Co-Crystal Structure of Wild Type Rat Polymerase Beta: Enzyme-Dna Binary Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na343

b:39.9
occ:1.00
 OG A:SER229 3.2 15.0 1.0
O A:LYS234 3.2 10.2 1.0
C A:LYS234 3.5 9.7 1.0
NZ A:LYS234 3.5 30.0 1.0
SD A:MET236 3.6 10.3 1.0
C5' T:DC7 3.6 10.9 1.0
O A:SER229 3.6 10.6 1.0
CB A:LYS234 3.7 26.1 1.0
N A:MET236 3.7 9.1 1.0
CB A:SER229 3.7 15.3 1.0
CD A:LYS234 3.8 27.9 1.0
C4' T:DC7 3.8 10.5 1.0
CG A:MET236 3.8 9.7 1.0
C A:SER229 3.8 11.2 1.0
CE A:LYS234 3.8 29.3 1.0
C A:PHE235 3.9 9.3 1.0
N A:PHE235 4.0 9.4 1.0
CA A:PHE235 4.0 9.5 1.0
CB A:MET236 4.0 9.9 1.0
N A:LYS230 4.2 10.8 1.0
CG A:LYS234 4.2 26.8 1.0
CA A:LYS234 4.2 9.6 1.0
CA A:SER229 4.3 11.7 1.0
CA A:MET236 4.5 9.2 1.0
O4' T:DC7 4.5 10.7 1.0
CA A:LYS230 4.6 10.7 1.0
O A:PHE235 4.6 9.1 1.0
O3' T:DC7 4.7 10.3 1.0
N A:GLY231 4.8 11.9 1.0
C3' T:DC7 4.9 10.2 1.0
O5' T:DC7 4.9 10.9 1.0
N A:SER229 5.0 11.4 1.0

Reference:

S.Rangarajan, C.L.Gridley, S.Firbank, S.Dalal, J.B.Sweasy, J.Jaeger. Crystallographic Studies of K72E Mutant Dna Polymerase Explain Loss of Lyase Function and Reveal Changes in the Overall Conformational State of the Polymerase Domain To Be Published.
Page generated: Mon Oct 7 13:39:13 2024

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