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Sodium in PDB 4ubh: Resting State of Rat Cysteine Dioxygenase Y157F Variant

Enzymatic activity of Resting State of Rat Cysteine Dioxygenase Y157F Variant

All present enzymatic activity of Resting State of Rat Cysteine Dioxygenase Y157F Variant:
1.13.11.20;

Protein crystallography data

The structure of Resting State of Rat Cysteine Dioxygenase Y157F Variant, PDB code: 4ubh was solved by E.P.Tchesnokov, M.Fellner, G.N.L.Jameson, S.M.Wilbanks, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.84 / 1.81
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 57.790, 57.790, 121.990, 90.00, 90.00, 90.00
R / Rfree (%) 19 / 23.3

Other elements in 4ubh:

The structure of Resting State of Rat Cysteine Dioxygenase Y157F Variant also contains other interesting chemical elements:

Iron (Fe) 1 atom
Chlorine (Cl) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Resting State of Rat Cysteine Dioxygenase Y157F Variant (pdb code 4ubh). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Resting State of Rat Cysteine Dioxygenase Y157F Variant, PDB code: 4ubh:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 4ubh

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Sodium binding site 1 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na302

b:19.4
occ:1.00
 OD1 A:ASP135 2.6 10.5 1.0
O A:GLY138 2.6 11.5 1.0
ND1 A:HIS88 2.9 12.4 1.0
C A:ASN134 3.4 11.1 1.0
CA A:ASP135 3.4 8.8 1.0
N A:ASP135 3.4 11.5 1.0
O A:ASN134 3.4 14.5 1.0
N A:HIS88 3.6 8.5 1.0
CG A:ASP135 3.7 10.4 1.0
CA A:ASP87 3.8 8.8 1.0
C A:GLY138 3.8 10.8 1.0
CE1 A:HIS88 3.8 11.9 1.0
CG A:HIS88 3.9 12.3 1.0
C A:ASP87 4.0 9.8 1.0
CB A:HIS88 4.1 12.0 1.0
CB A:ASP135 4.1 9.4 1.0
CA A:ASN134 4.2 11.6 1.0
CB A:ASP87 4.3 9.4 1.0
CG1 A:ILE133 4.4 13.3 1.0
CD1 A:ILE133 4.4 10.1 1.0
CA A:LEU139 4.4 14.4 1.0
CA A:HIS88 4.5 11.6 1.0
O A:HIS86 4.5 7.8 1.0
N A:LEU139 4.5 10.1 1.0
C A:ASP135 4.6 17.9 1.0
CD2 A:LEU139 4.6 9.8 1.0
N A:ASN134 4.6 10.9 1.0
OD2 A:ASP135 4.7 14.0 1.0
CG2 A:ILE133 4.8 7.4 1.0
N A:GLY138 4.8 12.8 1.0
CA A:GLY138 4.9 10.9 1.0
O A:ASP87 4.9 11.6 1.0
O A:ASP135 4.9 13.0 1.0
N A:ASP87 5.0 8.1 1.0
O A:HOH548 5.0 14.6 1.0
NE2 A:HIS88 5.0 4.8 1.0

Sodium binding site 2 out of 10 in 4ubh

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Sodium binding site 2 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na303

b:15.6
occ:1.00
 O A:CYS76 2.7 6.4 1.0
O A:ARG57 2.8 7.5 1.0
N A:ASP54 3.0 11.3 1.0
O A:ASP54 3.1 9.4 1.0
C A:CYS76 3.7 5.8 1.0
CA A:TYR58 3.7 8.9 1.0
CD2 A:PHE53 3.7 8.9 1.0
CA A:PHE53 3.7 9.2 1.0
ND1 A:HIS81 3.7 8.5 1.0
C A:ARG57 3.8 9.1 1.0
C A:PHE53 3.8 14.5 1.0
N A:THR59 3.8 8.7 1.0
CA A:ASP54 3.8 8.8 1.0
O A:HOH562 3.8 14.7 1.0
C A:ASP54 3.9 10.2 1.0
CB A:PHE53 3.9 10.8 1.0
N A:GLY78 3.9 8.0 1.0
CG2 A:THR59 3.9 8.3 1.0
CE1 A:HIS81 3.9 7.3 1.0
OG1 A:THR59 4.0 9.7 1.0
C A:TYR58 4.1 6.5 1.0
CG A:PHE53 4.1 9.3 1.0
CB A:ASP54 4.1 9.0 1.0
N A:TYR58 4.2 10.8 1.0
CB A:CYS76 4.3 6.8 1.0
N A:TRP77 4.3 7.8 1.0
CB A:THR59 4.4 6.8 1.0
CA A:TRP77 4.4 6.7 1.0
C A:TRP77 4.6 5.3 1.0
CA A:CYS76 4.6 5.8 1.0
CE2 A:PHE53 4.6 7.9 1.0
CA A:GLY78 4.7 10.3 1.0
CA A:THR59 4.7 6.2 1.0
CB A:TYR58 4.8 8.2 1.0
O A:LYS52 4.9 7.4 1.0
O A:TYR58 5.0 7.7 1.0
N A:PHE53 5.0 6.7 1.0
CA A:ARG57 5.0 11.0 1.0

Sodium binding site 3 out of 10 in 4ubh

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Sodium binding site 3 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na304

b:20.0
occ:1.00
 O A:HOH553 2.8 17.7 1.0
N A:ALA13 3.0 12.2 1.0
O A:HOH646 3.0 29.0 1.0
O A:HOH660 3.1 32.2 1.0
N A:LEU12 3.4 13.7 1.0
CB A:THR11 3.5 14.2 1.0
CB A:LEU12 3.5 11.6 1.0
CB A:ALA13 3.5 15.6 1.0
CD A:GLU46 3.7 14.7 1.0
OG1 A:THR11 3.7 9.0 1.0
CG A:GLU46 3.7 11.5 1.0
CA A:LEU12 3.7 13.4 1.0
OE1 A:GLU46 3.8 13.4 1.0
CB A:GLU46 3.8 8.7 1.0
C A:LEU12 3.8 11.8 1.0
CA A:ALA13 3.8 13.6 1.0
C A:THR11 4.1 10.1 1.0
OE2 A:GLU46 4.2 18.0 1.0
CA A:THR11 4.4 12.3 1.0
CG2 A:THR11 4.5 20.5 1.0
CG A:LEU12 4.6 12.0 1.0
CA A:GLU46 4.7 5.8 1.0
O A:GLU46 4.8 9.5 1.0
O A:HOH566 4.8 24.4 1.0
O A:HOH612 5.0 26.9 1.0
O A:LEU12 5.0 8.8 1.0

Sodium binding site 4 out of 10 in 4ubh

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Sodium binding site 4 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na305

b:16.2
occ:1.00
 OD1 A:ASN144 2.8 10.7 1.0
O A:HOH446 2.8 19.6 1.0
O A:GLU149 2.9 15.2 1.0
N A:ASN101 3.1 14.1 1.0
O A:ASN101 3.2 10.4 1.0
CG A:ASN144 3.5 7.6 1.0
CB A:SER146 3.5 11.6 1.0
ND2 A:ASN144 3.7 6.1 1.0
CA A:GLY100 3.8 14.5 1.0
C A:GLU149 3.8 11.7 1.0
CB A:ALA151 3.8 8.8 1.0
CB A:GLU149 3.9 15.3 1.0
O A:PRO150 3.9 11.1 1.0
C A:GLY100 4.0 12.2 1.0
C A:ASN101 4.0 11.1 1.0
CA A:ASN101 4.0 11.6 1.0
OG A:SER146 4.1 9.2 1.0
C A:PRO150 4.1 8.1 1.0
N A:ALA151 4.3 7.4 1.0
CA A:ALA151 4.3 14.4 1.0
O A:HOH440 4.3 11.2 1.0
CA A:GLU149 4.4 13.3 1.0
CB A:ASN101 4.5 17.6 1.0
CB A:ASN144 4.8 10.5 1.0
N A:PRO150 4.8 11.0 1.0
ND2 A:ASN101 4.8 17.5 1.0
O A:HOH488 4.8 19.2 1.0
CA A:SER146 4.8 9.6 1.0
CA A:PRO150 4.9 13.1 1.0
N A:SER146 4.9 13.5 1.0

Sodium binding site 5 out of 10 in 4ubh

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Sodium binding site 5 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na306

b:16.6
occ:1.00
 OE1 A:GLU143 2.7 20.8 1.0
OG1 A:THR105 2.8 13.3 1.0
O A:LYS103 2.9 8.6 1.0
O A:ARG141 3.1 10.9 1.0
N A:THR105 3.3 12.0 1.0
CG A:GLU143 3.4 11.7 1.0
CD A:GLU143 3.5 26.1 1.0
CB A:THR105 3.5 11.3 1.0
C A:LYS103 3.5 11.2 1.0
C A:ARG141 3.6 11.1 1.0
CE A:LYS103 3.7 30.3 1.0
C A:GLU104 3.8 11.1 1.0
O A:HOH594 3.9 31.7 1.0
CB A:GLU143 3.9 11.6 1.0
CG A:LYS103 4.0 17.6 1.0
CA A:GLU104 4.0 9.4 1.0
N A:GLU143 4.0 6.4 1.0
CA A:THR105 4.0 10.6 1.0
CB A:ARG141 4.1 9.8 1.0
N A:GLU104 4.1 9.6 1.0
CD A:ARG141 4.1 19.2 1.0
CB A:LYS103 4.1 13.6 1.0
N A:VAL142 4.2 9.1 1.0
CA A:VAL142 4.2 6.6 1.0
C A:VAL142 4.2 8.1 1.0
CG A:ARG141 4.3 13.5 1.0
CA A:ARG141 4.4 9.9 1.0
CA A:LYS103 4.5 11.0 1.0
CD A:LYS103 4.5 20.4 1.0
CA A:GLU143 4.6 9.1 1.0
OE2 A:GLU143 4.7 27.6 1.0
O A:GLU104 4.7 14.9 1.0
NZ A:LYS103 4.9 35.0 1.0
CG2 A:THR105 4.9 13.1 1.0

Sodium binding site 6 out of 10 in 4ubh

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Sodium binding site 6 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na307

b:16.5
occ:1.00
 N A:ARG60 2.9 5.3 1.0
O A:THR180 3.0 17.6 1.0
CA A:THR59 3.6 6.2 1.0
CB A:HIS182 3.6 11.6 1.0
N A:HIS182 3.6 11.4 1.0
C A:THR59 3.7 6.8 1.0
CB A:ARG60 3.7 8.8 1.0
CA A:ARG60 3.8 6.3 1.0
O A:ARG60 3.9 11.3 1.0
CG A:ARG60 4.0 13.4 1.0
CA A:HIS182 4.1 13.4 1.0
C A:THR180 4.1 21.6 1.0
CB A:THR59 4.2 6.8 1.0
OG1 A:THR180 4.3 33.2 1.0
O A:TYR58 4.3 7.7 1.0
C A:PHE181 4.3 15.6 1.0
NH2 A:ARG57 4.3 32.6 1.0
C A:ARG60 4.4 8.5 1.0
CA A:PHE181 4.6 17.4 1.0
CG A:HIS182 4.6 10.4 1.0
O A:HOH626 4.7 31.7 1.0
CG2 A:THR59 4.7 8.3 1.0
CD A:ARG60 4.7 18.7 1.0
N A:THR59 4.7 8.7 1.0
N A:PHE181 4.8 22.8 1.0
CZ A:ARG57 4.8 31.8 1.0
ND1 A:HIS182 4.8 14.0 1.0
O A:THR59 4.9 5.8 1.0
C A:TYR58 4.9 6.5 1.0

Sodium binding site 7 out of 10 in 4ubh

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Sodium binding site 7 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na308

b:18.4
occ:1.00
 OG A:SER183 2.8 7.4 1.0
N A:GLY186 2.9 8.0 1.0
O A:LEU62 2.9 8.1 1.0
CD1 A:TYR50 3.3 14.2 1.0
N A:PHE185 3.4 12.7 1.0
CA A:GLY186 3.5 13.0 1.0
CB A:SER183 3.6 10.0 1.0
C A:SER183 3.7 15.9 1.0
C A:LYS184 3.7 13.8 1.0
N A:LYS184 3.7 11.6 1.0
CB A:ASN61 3.8 4.8 1.0
N A:LEU62 3.8 10.1 1.0
C A:LEU62 3.8 11.5 1.0
O A:SER183 3.8 9.4 1.0
CA A:LYS184 3.8 12.2 1.0
C A:PHE185 3.9 16.5 1.0
C A:ASN61 3.9 10.6 1.0
CA A:PHE185 4.0 16.2 1.0
CE1 A:TYR50 4.1 13.8 1.0
CA A:ASN61 4.1 6.6 1.0
CB A:TYR50 4.2 6.0 1.0
CG A:TYR50 4.2 11.9 1.0
CA A:SER183 4.3 11.4 1.0
CA A:TYR50 4.3 10.2 1.0
O A:ASN61 4.4 13.1 1.0
C A:GLY186 4.4 14.8 1.0
CA A:LEU62 4.4 11.8 1.0
O A:LYS184 4.4 10.4 1.0
N A:ILE187 4.5 12.7 1.0
OD1 A:ASN61 4.6 6.6 1.0
CG A:ASN61 4.7 10.4 1.0
O A:TYR50 4.8 10.2 1.0
CE A:LYS52 4.8 23.6 1.0
N A:VAL63 4.8 7.8 1.0

Sodium binding site 8 out of 10 in 4ubh

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Sodium binding site 8 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na309

b:20.8
occ:1.00
 O A:HOH738 2.4 37.0 1.0
O A:PRO9 2.6 16.3 1.0
N A:GLU41 2.9 10.3 1.0
O A:HOH583 2.9 19.8 1.0
NZ A:LYS8 3.4 32.5 1.0
CD1 A:TYR40 3.6 8.9 1.0
CB A:GLU41 3.6 17.4 1.0
O A:ARG10 3.7 18.4 1.0
CA A:TYR40 3.7 9.4 1.0
CA A:GLU41 3.7 13.6 1.0
C A:TYR40 3.8 12.4 1.0
C A:PRO9 3.8 12.7 1.0
C A:ARG10 3.9 13.3 1.0
O A:GLU41 3.9 9.4 1.0
CE A:LYS8 4.0 36.2 1.0
O A:ALA39 4.0 11.0 1.0
CG A:GLU41 4.2 25.5 1.0
CA A:ARG10 4.2 19.5 1.0
CE1 A:TYR40 4.3 7.7 1.0
C A:GLU41 4.3 7.7 1.0
N A:ARG10 4.4 9.8 1.0
CG A:TYR40 4.5 10.2 1.0
CB A:TYR40 4.6 8.6 1.0
N A:THR11 4.6 17.8 1.0
CG A:LYS8 4.7 22.0 1.0
CD A:GLU41 4.7 47.5 1.0
N A:TYR40 4.8 10.5 1.0
C A:ALA39 4.8 13.3 1.0
O A:HOH552 4.9 17.0 1.0
CA A:PRO9 4.9 12.6 1.0
O A:TYR40 5.0 11.7 1.0
CD A:LYS8 5.0 34.1 1.0

Sodium binding site 9 out of 10 in 4ubh

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Sodium binding site 9 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F 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 Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na310

b:18.1
occ:1.00
 O A:GLY82 2.8 11.2 1.0
O A:HOH545 2.9 16.9 1.0
N A:TYR58 3.1 10.8 1.0
N A:GLY82 3.3 12.9 1.0
CD1 A:TYR58 3.3 11.6 1.0
O A:HOH656 3.4 31.8 1.0
CB A:ARG57 3.5 10.6 1.0
CA A:ARG57 3.5 11.0 1.0
CB A:HIS81 3.6 7.3 1.0
C A:GLY82 3.8 8.1 1.0
C A:ARG57 3.8 9.1 1.0
CA A:HIS81 3.9 10.4 1.0
C A:HIS81 4.0 9.4 1.0
CG A:HIS81 4.1 8.4 1.0
CA A:GLY82 4.1 9.8 1.0
CB A:TYR58 4.1 8.2 1.0
CE1 A:TYR58 4.2 16.7 1.0
CG A:TYR58 4.2 10.4 1.0
CA A:TYR58 4.2 8.9 1.0
CD2 A:HIS81 4.6 7.6 1.0
O A:TYR56 4.6 15.6 1.0
ND1 A:HIS81 4.7 8.5 1.0
CG A:ARG57 4.8 13.4 1.0
N A:ARG57 4.8 9.6 1.0
N A:SER83 4.9 8.8 1.0
NE A:ARG57 4.9 21.6 1.0
O A:HOH640 4.9 35.6 1.0
O A:ARG57 5.0 7.5 1.0

Sodium binding site 10 out of 10 in 4ubh

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Sodium binding site 10 out of 10 in the Resting State of Rat Cysteine Dioxygenase Y157F Variant


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Resting State of Rat Cysteine Dioxygenase Y157F Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na312

b:41.0
occ:1.00
 O A:HOH686 2.5 35.2 1.0
O A:HOH524 2.8 37.0 1.0
NE2 A:HIS165 2.9 20.1 1.0
O A:HOH669 3.2 47.0 1.0
CD2 A:HIS165 3.6 13.8 1.0
CE1 A:HIS165 4.0 19.5 1.0
O A:HOH473 4.3 40.8 1.0
CE A:LYS174 4.3 30.4 1.0
CB A:LYS176 4.3 28.7 1.0
CD A:LYS176 4.4 33.6 1.0
O A:HOH741 4.4 40.1 1.0
O A:HOH743 4.5 37.4 1.0
CG A:LYS176 4.5 28.1 1.0
CG A:HIS165 4.9 18.9 1.0
NZ A:LYS174 5.0 39.2 1.0
CE A:LYS176 5.0 41.1 1.0

Reference:

E.P.Tchesnokov, M.Fellner, G.N.L.Jameson, S.M.Wilbanks. Crystal Structure of Cysteine Dioxygenase Mutant To Be Published.
Page generated: Tue Dec 15 07:40:46 2020

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