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Sodium in PDB 4ubg: Resting State of Rat Cysteine Dioxygenase C93G Variant

Enzymatic activity of Resting State of Rat Cysteine Dioxygenase C93G Variant

All present enzymatic activity of Resting State of Rat Cysteine Dioxygenase C93G Variant:
1.13.11.20;

Protein crystallography data

The structure of Resting State of Rat Cysteine Dioxygenase C93G Variant, PDB code: 4ubg was solved by M.Fellner, E.P.Tchesnokov, G.N.Jameson, S.M.Wilbanks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.10 / 1.90
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.840, 57.840, 122.730, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 24.1

Other elements in 4ubg:

The structure of Resting State of Rat Cysteine Dioxygenase C93G Variant also contains other interesting chemical elements:

Iron (Fe) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Resting State of Rat Cysteine Dioxygenase C93G Variant (pdb code 4ubg). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 9 binding sites of Sodium where determined in the Resting State of Rat Cysteine Dioxygenase C93G Variant, PDB code: 4ubg:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Sodium binding site 1 out of 9 in 4ubg

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Sodium binding site 1 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:30.0
occ:1.00
N A:ASP54 2.8 13.8 1.0
O A:ARG57 2.9 12.2 1.0
O A:ASP54 2.9 10.7 1.0
O A:CYS76 3.0 11.6 1.0
CA A:PHE53 3.6 13.8 1.0
O A:HOH503 3.6 16.7 1.0
C A:ASP54 3.7 18.6 1.0
C A:PHE53 3.7 17.6 1.0
CD1 A:PHE53 3.7 15.9 1.0
CA A:ASP54 3.7 13.5 1.0
CB A:PHE53 3.8 10.7 1.0
ND1 A:HIS81 3.8 11.8 1.0
CA A:TYR58 3.8 9.2 1.0
C A:ARG57 3.8 9.4 1.0
C A:CYS76 3.9 13.0 1.0
CG2 A:THR59 3.9 10.0 1.0
N A:GLY78 4.0 11.1 1.0
CE1 A:HIS81 4.0 14.2 1.0
N A:THR59 4.0 7.7 1.0
CB A:ASP54 4.1 12.7 1.0
CG A:PHE53 4.1 13.1 1.0
OG1 A:THR59 4.2 16.8 1.0
C A:TYR58 4.2 12.3 1.0
N A:TYR58 4.3 13.8 1.0
CB A:CYS76 4.4 10.2 1.0
N A:TRP77 4.5 11.9 1.0
CB A:THR59 4.6 10.0 1.0
CA A:TRP77 4.6 11.6 1.0
C A:TRP77 4.6 11.2 1.0
CE1 A:PHE53 4.7 14.6 1.0
CA A:GLY78 4.7 12.7 1.0
CA A:CYS76 4.8 10.0 1.0
O A:PHE53 4.9 12.8 1.0
CA A:THR59 4.9 10.3 1.0
CB A:TYR58 4.9 9.5 1.0
N A:PHE53 4.9 11.7 1.0
N A:GLN55 5.0 14.5 1.0

Sodium binding site 2 out of 9 in 4ubg

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Sodium binding site 2 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:30.0
occ:1.00
O A:GLY138 2.6 21.6 1.0
OD1 A:ASP135 2.6 13.9 1.0
ND1 A:HIS88 2.8 19.2 1.0
CA A:ASP135 3.5 20.4 1.0
N A:HIS88 3.5 15.7 1.0
CA A:ASP87 3.6 15.8 1.0
N A:ASP135 3.7 13.9 1.0
O A:ASN134 3.7 14.0 1.0
CE1 A:HIS88 3.7 19.1 1.0
C A:ASN134 3.7 15.5 1.0
C A:GLY138 3.7 16.9 1.0
CG A:ASP135 3.7 13.3 1.0
C A:ASP87 3.8 14.2 1.0
CG A:HIS88 3.8 18.3 1.0
CB A:HIS88 4.1 16.8 1.0
CA A:LEU139 4.1 22.0 1.0
O A:HIS86 4.2 14.2 1.0
CB A:ASP87 4.2 12.8 1.0
CB A:ASP135 4.2 13.2 1.0
CG1 A:ILE133 4.3 26.7 1.0
N A:LEU139 4.3 16.6 1.0
CD2 A:LEU139 4.4 18.4 1.0
CA A:HIS88 4.4 15.9 1.0
CA A:ASN134 4.6 16.3 1.0
C A:ASP135 4.6 21.6 1.0
CD1 A:ILE133 4.6 21.0 1.0
N A:ASP87 4.7 15.6 1.0
O A:ASP87 4.7 11.8 1.0
OD2 A:ASP135 4.8 18.0 1.0
O A:ASP135 4.8 20.0 1.0
CA A:GLY138 4.9 18.5 1.0
C A:HIS86 4.9 16.1 1.0
NE2 A:HIS88 4.9 20.7 1.0
CZ2 A:TRP109 4.9 18.5 1.0
C A:LEU139 4.9 15.7 1.0
N A:GLY138 4.9 18.4 1.0
CD2 A:HIS88 5.0 19.2 1.0
N A:ASN134 5.0 22.4 1.0

Sodium binding site 3 out of 9 in 4ubg

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Sodium binding site 3 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:30.0
occ:1.00
OD1 A:ASN144 2.7 13.8 1.0
O A:HOH414 2.9 18.7 1.0
O A:GLU149 2.9 16.5 1.0
O A:ASN101 3.2 12.2 1.0
N A:ASN101 3.2 15.8 1.0
CG A:ASN144 3.5 11.9 1.0
CB A:SER146 3.5 12.3 1.0
ND2 A:ASN144 3.7 12.4 1.0
CB A:ALA151 3.7 10.8 1.0
CA A:GLY100 3.8 14.4 1.0
C A:GLU149 3.9 14.7 1.0
CB A:GLU149 3.9 18.9 1.0
O A:PRO150 4.0 16.9 1.0
C A:GLY100 4.0 12.8 1.0
C A:ASN101 4.0 13.9 1.0
CA A:ASN101 4.1 15.6 1.0
C A:PRO150 4.1 11.3 1.0
OG A:SER146 4.1 13.6 1.0
N A:ALA151 4.2 12.5 1.0
CA A:ALA151 4.2 13.6 1.0
O A:HOH427 4.3 14.9 1.0
CA A:GLU149 4.5 18.0 1.0
CB A:ASN101 4.5 16.4 1.0
ND2 A:ASN101 4.6 15.5 1.0
CB A:ASN144 4.8 15.5 1.0
N A:PRO150 4.8 11.2 1.0
O A:HOH458 4.8 24.6 1.0
CA A:SER146 4.8 10.0 1.0
CA A:PRO150 4.9 17.1 1.0
N A:SER146 4.9 18.6 1.0

Sodium binding site 4 out of 9 in 4ubg

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Sodium binding site 4 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:30.0
occ:1.00
OG1 A:THR105 2.6 19.0 1.0
OE1 A:GLU143 2.6 27.7 1.0
O A:LYS103 3.0 14.9 1.0
CG A:GLU143 3.3 18.5 1.0
O A:ARG141 3.3 15.2 1.0
CD A:GLU143 3.4 26.8 1.0
O A:HOH520 3.4 40.9 1.0
N A:THR105 3.4 15.8 1.0
CB A:THR105 3.5 15.8 1.0
C A:LYS103 3.7 15.8 1.0
CE A:LYS103 3.7 29.9 1.0
C A:ARG141 3.8 16.0 1.0
CG A:LYS103 3.9 16.0 1.0
CB A:GLU143 3.9 14.8 1.0
C A:GLU104 4.0 14.0 1.0
N A:GLU143 4.0 11.7 1.0
CB A:ARG141 4.1 18.2 1.0
CA A:THR105 4.1 17.3 1.0
CA A:GLU104 4.1 9.1 1.0
CD A:ARG141 4.2 19.0 1.0
CB A:LYS103 4.2 15.5 1.0
N A:GLU104 4.2 13.4 1.0
N A:VAL142 4.3 10.8 1.0
CA A:VAL142 4.3 11.7 1.0
C A:VAL142 4.3 11.8 1.0
CD A:LYS103 4.4 23.1 1.0
CG A:ARG141 4.5 25.6 1.0
CA A:ARG141 4.5 8.3 1.0
CA A:LYS103 4.6 16.4 1.0
OE2 A:GLU143 4.6 37.5 1.0
CA A:GLU143 4.6 13.6 1.0
NZ A:LYS103 4.7 30.1 1.0
O A:HOH522 4.8 39.8 1.0
O A:GLU104 4.8 13.5 1.0
CG2 A:THR105 4.8 20.6 1.0
NE A:ARG141 4.9 22.6 1.0

Sodium binding site 5 out of 9 in 4ubg

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Sodium binding site 5 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:30.0
occ:1.00
O A:HOH516 2.8 32.0 1.0
N A:ALA13 2.8 17.4 1.0
O A:HOH532 2.9 31.2 1.0
N A:LEU12 3.2 20.1 1.0
CB A:THR11 3.4 13.4 1.0
CB A:ALA13 3.5 22.3 1.0
OG1 A:THR11 3.5 20.0 1.0
CB A:LEU12 3.5 14.3 1.0
CA A:LEU12 3.7 20.0 1.0
CG A:GLU46 3.7 20.6 1.0
CD A:GLU46 3.7 19.0 1.0
C A:LEU12 3.7 13.3 1.0
CA A:ALA13 3.7 15.3 1.0
OE1 A:GLU46 3.8 15.8 1.0
CB A:GLU46 3.9 14.2 1.0
C A:THR11 4.0 18.0 1.0
O A:HOH517 4.0 35.8 1.0
OE2 A:GLU46 4.2 23.9 1.0
CA A:THR11 4.2 15.6 1.0
O A:HOH611 4.3 21.4 1.0
CG2 A:THR11 4.5 15.4 1.0
CG A:LEU12 4.6 18.1 1.0
O A:LEU12 4.9 12.8 1.0
CA A:GLU46 4.9 11.3 1.0
O A:THR11 4.9 11.4 1.0
C A:ALA13 4.9 17.6 1.0
N A:ASP14 4.9 16.2 1.0
O A:HOH535 5.0 30.2 1.0
O A:GLU46 5.0 9.7 1.0

Sodium binding site 6 out of 9 in 4ubg

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Sodium binding site 6 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:30.0
occ:1.00
N A:ARG60 2.9 9.2 0.5
N A:ARG60 2.9 9.2 0.5
O A:THR180 3.1 23.7 1.0
CA A:THR59 3.5 10.3 1.0
N A:HIS182 3.6 16.0 1.0
CB A:HIS182 3.6 13.0 1.0
C A:THR59 3.7 12.0 1.0
CB A:ARG60 3.7 9.7 0.5
CB A:ARG60 3.7 9.8 0.5
CA A:ARG60 3.8 11.2 0.5
CA A:ARG60 3.8 11.0 0.5
CG A:ARG60 3.9 14.5 0.5
O A:ARG60 3.9 12.8 0.5
O A:ARG60 3.9 13.0 0.5
CG A:ARG60 4.0 14.6 0.5
NH2 A:ARG57 4.1 30.2 1.0
CA A:HIS182 4.1 14.6 1.0
CB A:THR59 4.2 10.0 1.0
C A:THR180 4.2 29.6 1.0
O A:TYR58 4.2 9.4 1.0
CD A:ARG60 4.2 16.9 0.5
C A:ARG60 4.3 12.6 0.5
C A:ARG60 4.3 12.7 0.5
C A:PHE181 4.3 20.5 1.0
OG1 A:THR180 4.5 44.1 1.0
CA A:PHE181 4.6 18.9 1.0
CZ A:ARG57 4.7 34.7 1.0
N A:THR59 4.7 7.7 1.0
CG A:HIS182 4.7 13.9 1.0
CG2 A:THR59 4.7 10.0 1.0
CD A:ARG60 4.8 14.9 0.5
N A:PHE181 4.8 28.7 1.0
O A:THR59 4.8 9.9 1.0
C A:TYR58 4.9 12.3 1.0
ND1 A:HIS182 5.0 22.4 1.0

Sodium binding site 7 out of 9 in 4ubg

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Sodium binding site 7 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:30.0
occ:1.00
N A:GLY186 2.8 15.0 1.0
OG A:SER183 2.8 14.6 1.0
O A:LEU62 2.9 11.7 1.0
N A:PHE185 3.2 14.7 1.0
CD1 A:TYR50 3.4 17.3 1.0
CA A:GLY186 3.5 15.8 1.0
C A:LYS184 3.6 16.4 1.0
C A:SER183 3.6 18.1 1.0
CB A:SER183 3.6 11.8 1.0
N A:LYS184 3.6 13.6 1.0
O A:SER183 3.7 12.9 1.0
CA A:LYS184 3.7 17.3 1.0
C A:PHE185 3.8 21.0 1.0
CA A:PHE185 3.9 16.0 1.0
C A:LEU62 3.9 10.8 1.0
CB A:ASN61 3.9 9.8 1.0
N A:LEU62 3.9 16.1 1.0
C A:ASN61 4.0 17.0 1.0
CE1 A:TYR50 4.1 14.7 1.0
CA A:ASN61 4.2 10.3 1.0
CA A:SER183 4.2 16.0 1.0
CG A:TYR50 4.3 11.9 1.0
CB A:TYR50 4.3 12.5 1.0
C A:GLY186 4.3 14.8 1.0
O A:LYS184 4.3 14.5 1.0
CA A:TYR50 4.4 15.8 1.0
O A:ASN61 4.4 14.6 1.0
N A:ILE187 4.4 15.2 1.0
CA A:LEU62 4.5 13.4 1.0
OD1 A:ASN61 4.8 14.5 1.0
CG A:ASN61 4.8 15.3 1.0
CE A:LYS52 4.9 19.1 1.0
N A:VAL63 4.9 10.2 1.0
O A:PHE185 4.9 20.6 1.0
O A:TYR50 5.0 15.7 1.0

Sodium binding site 8 out of 9 in 4ubg

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Sodium binding site 8 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:30.0
occ:1.00
O A:GLY82 2.9 13.2 1.0
O A:HOH482 3.0 20.1 1.0
N A:TYR58 3.0 13.8 1.0
CD2 A:TYR58 3.3 9.7 1.0
CB A:ARG57 3.3 15.4 1.0
CA A:ARG57 3.4 12.5 1.0
N A:GLY82 3.4 14.9 1.0
CB A:HIS81 3.5 13.2 1.0
C A:ARG57 3.7 9.4 1.0
C A:GLY82 3.8 14.5 1.0
CA A:HIS81 3.9 13.2 1.0
O A:HOH528 3.9 28.8 1.0
CG A:HIS81 3.9 8.6 1.0
C A:HIS81 4.0 10.4 1.0
O A:HOH546 4.0 29.4 1.0
CB A:TYR58 4.2 9.5 1.0
CA A:TYR58 4.2 9.2 1.0
CE2 A:TYR58 4.2 15.4 1.0
CA A:GLY82 4.2 14.0 1.0
CG A:TYR58 4.2 12.5 1.0
CD2 A:HIS81 4.5 9.2 1.0
ND1 A:HIS81 4.6 11.8 1.0
O A:TYR56 4.6 17.4 1.0
CG A:ARG57 4.7 15.1 1.0
N A:ARG57 4.7 13.3 1.0
NE A:ARG57 4.8 26.4 1.0
O A:ARG57 4.9 12.2 1.0
CD A:ARG57 5.0 26.1 1.0
N A:SER83 5.0 11.7 1.0

Sodium binding site 9 out of 9 in 4ubg

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Sodium binding site 9 out of 9 in the Resting State of Rat Cysteine Dioxygenase C93G Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Resting State of Rat Cysteine Dioxygenase C93G Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:30.0
occ:1.00
O A:PRO9 2.5 16.0 1.0
N A:GLU41 2.9 13.0 1.0
O A:HOH501 3.0 22.7 1.0
NZ A:LYS8 3.3 29.4 1.0
CB A:GLU41 3.6 24.2 1.0
CD1 A:TYR40 3.7 14.3 1.0
CE A:LYS8 3.7 41.3 1.0
O A:ARG10 3.7 23.3 1.0
C A:PRO9 3.7 17.9 1.0
CA A:GLU41 3.8 17.3 1.0
CA A:TYR40 3.8 17.4 1.0
C A:TYR40 3.8 17.5 1.0
O A:ALA39 3.9 14.3 1.0
C A:ARG10 4.0 15.2 1.0
O A:GLU41 4.0 12.5 1.0
CA A:ARG10 4.2 22.3 1.0
CG A:GLU41 4.2 31.0 1.0
CE1 A:TYR40 4.3 13.0 1.0
C A:GLU41 4.4 13.6 1.0
N A:ARG10 4.4 11.3 1.0
CG A:TYR40 4.5 17.1 1.0
CG A:LYS8 4.5 17.0 1.0
CB A:TYR40 4.6 15.2 1.0
N A:THR11 4.7 16.1 1.0
CD A:LYS8 4.8 28.4 1.0
C A:ALA39 4.8 13.8 1.0
CD A:GLU41 4.8 57.4 1.0
N A:TYR40 4.8 13.4 1.0
CA A:PRO9 4.8 18.4 1.0
OE2 A:GLU41 4.9 54.4 1.0
O A:TYR40 5.0 14.6 1.0
O A:HOH510 5.0 21.8 1.0

Reference:

C.G.Davies, M.Fellner, E.P.Tchesnokov, S.M.Wilbanks, G.N.Jameson. The Cys-Tyr Crosslink of Cysteine Dioxygenase Changes the Optimum pH of Reaction Without Structural Change Biochemistry 2014.
ISSN: ISSN 0006-2960
Page generated: Tue Dec 15 07:40:46 2020

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