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Sodium in PDB 7rjp: Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt

Enzymatic activity of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt

All present enzymatic activity of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt:
2.1.2.1;

Protein crystallography data

The structure of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt, PDB code: 7rjp was solved by E.Fedorov, K.Islam, A.Ghosh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 25.07 / 1.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 43.043, 51.56, 57.384, 90, 90, 90
R / Rfree (%) 14.8 / 17.4

Other elements in 7rjp:

The structure of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt (pdb code 7rjp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 8 binding sites of Sodium where determined in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt, PDB code: 7rjp:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Sodium binding site 1 out of 8 in 7rjp

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Sodium binding site 1 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na202

b:15.3
occ:1.00
O A:HOH350 2.8 7.5 1.0
HB2 A:LEU67 2.8 6.9 1.0
O A:LEU63 2.9 5.2 1.0
HB3 A:LEU114 2.9 5.7 1.0
HD22 A:LEU114 3.0 5.9 1.0
HB3 A:LEU67 3.1 6.9 1.0
HD22 A:LEU67 3.1 10.6 1.0
HE22 A:GLN59 3.2 18.9 0.6
HA A:GLN64 3.2 5.4 1.0
HB3 A:LEU63 3.3 5.3 1.0
CB A:LEU67 3.4 5.8 1.0
C A:LEU63 3.5 4.2 1.0
HD23 A:LEU67 3.5 10.6 1.0
CD2 A:LEU67 3.7 8.8 1.0
OE1 A:GLN59 3.7 9.5 0.6
NE2 A:GLN59 3.7 15.7 0.6
CD2 A:LEU114 3.8 4.9 1.0
CB A:LEU114 3.9 4.8 1.0
HD23 A:LEU114 3.9 5.9 1.0
H A:LEU67 3.9 5.2 1.0
N A:GLN64 3.9 4.5 1.0
CA A:GLN64 4.0 4.5 1.0
CD A:GLN59 4.0 18.1 0.6
O A:LEU114 4.0 5.3 1.0
CB A:LEU63 4.1 4.4 1.0
CG A:LEU67 4.2 5.9 1.0
CA A:LEU63 4.3 4.2 1.0
HE21 A:GLN59 4.3 18.9 0.6
HA A:LEU114 4.3 5.5 1.0
HB2 A:LEU63 4.4 5.3 1.0
CG A:LEU114 4.4 5.1 1.0
HD13 A:LEU114 4.4 6.2 1.0
C A:LEU114 4.4 4.5 1.0
N A:LEU67 4.5 4.3 1.0
CA A:LEU114 4.5 4.6 1.0
HB2 A:LEU114 4.5 5.7 1.0
H A:GLN64 4.5 5.4 1.0
HD21 A:LEU114 4.5 5.9 1.0
CA A:LEU67 4.5 4.8 1.0
O A:HOH311 4.6 22.5 0.4
HD21 A:LEU67 4.6 10.6 1.0
HA A:LEU63 4.6 5.0 1.0
HD13 A:LEU67 4.7 8.5 1.0
C A:GLN64 4.7 4.4 1.0
O A:GLN64 4.8 5.1 1.0
HD22 A:LEU63 4.8 8.5 1.0
HG A:LEU67 4.9 7.1 1.0
CD1 A:LEU114 5.0 5.2 1.0
HB2 A:GLN64 5.0 7.1 1.0

Sodium binding site 2 out of 8 in 7rjp

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Sodium binding site 2 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na203

b:33.2
occ:1.00
O A:HOH451 2.7 33.2 1.0
HB2 A:LYS102 3.0 9.8 1.0
HG3 A:LYS102 3.4 12.1 1.0
HB3 A:LYS102 3.4 9.8 1.0
CB A:LYS102 3.6 8.1 1.0
CG A:LYS102 4.0 10.1 1.0
HG2 A:LYS102 4.4 12.1 1.0
O A:HOH355 4.9 9.0 1.0
HG1 A:THR103 4.9 8.9 1.0
CA A:LYS102 4.9 6.3 1.0
O1 A:EDO201 5.0 16.8 1.0

Sodium binding site 3 out of 8 in 7rjp

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Sodium binding site 3 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na204

b:38.6
occ:1.00
O A:PRO142 2.5 18.3 0.4
H A:GLY143 2.5 17.5 0.6
HA2 A:GLY143 2.7 22.9 0.6
O A:ASP144 2.8 12.5 1.0
HB2 A:LEU148 3.0 14.3 1.0
H A:LEU148 3.0 9.2 1.0
CA A:GLY143 3.1 19.1 0.6
N A:GLY143 3.1 14.6 0.6
O A:HOH304 3.1 26.7 1.0
C A:GLY143 3.1 16.5 0.6
H A:ASP144 3.2 17.9 0.4
HB A:VAL147 3.2 11.0 1.0
HA2 A:GLY143 3.3 19.6 0.4
O A:GLY143 3.5 17.0 0.6
N A:ASP144 3.5 14.9 1.0
N A:LEU148 3.5 7.7 1.0
C A:PRO142 3.6 13.8 0.4
C A:ASP144 3.7 11.5 1.0
H A:ASP144 3.7 17.9 0.6
CB A:LEU148 3.8 11.9 1.0
HG12 A:VAL147 3.8 12.0 1.0
C A:GLY143 3.9 16.0 0.4
CA A:GLY143 3.9 16.3 0.4
HB3 A:LEU148 3.9 14.3 1.0
HA3 A:GLY143 4.0 22.9 0.6
CA A:LEU148 4.1 10.3 1.0
CB A:VAL147 4.1 9.1 1.0
HA A:LEU148 4.1 12.4 1.0
N A:GLY143 4.2 12.3 0.4
HA A:PRO142 4.2 15.7 0.6
CA A:ASP144 4.3 12.0 1.0
C A:PRO142 4.3 11.8 0.6
C A:VAL147 4.3 7.0 1.0
CG1 A:VAL147 4.4 10.0 1.0
HA A:ASP145 4.4 10.4 1.0
H A:VAL147 4.5 8.7 1.0
HD12 A:LEU148 4.5 26.5 1.0
HA A:PRO142 4.6 15.5 0.4
CA A:VAL147 4.6 7.3 1.0
HG11 A:VAL147 4.6 12.0 1.0
O A:GLY143 4.6 18.3 0.4
N A:ASP145 4.7 9.6 1.0
CA A:PRO142 4.8 12.9 0.4
CA A:PRO142 4.8 13.1 0.6
O A:HOH317 4.8 25.1 1.0
HA3 A:GLY143 4.8 19.6 0.4
N A:VAL147 4.8 7.2 1.0
CA A:ASP145 4.9 8.7 1.0
HA A:ASP144 4.9 14.4 1.0
HB2 A:ASP144 5.0 14.5 1.0
HD13 A:LEU148 5.0 26.5 1.0
CG A:LEU148 5.0 19.7 1.0

Sodium binding site 4 out of 8 in 7rjp

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Sodium binding site 4 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na205

b:14.2
occ:1.00
H A:ARG58 2.1 6.3 1.0
HA A:LYS57 2.4 7.7 1.0
O A:TYR119 2.8 5.4 1.0
HB3 A:ASN117 2.9 8.6 1.0
N A:ARG58 2.9 5.3 1.0
O A:ASN117 2.9 5.6 1.0
HA A:TRP120 3.1 5.3 1.0
HE3 A:TRP120 3.2 7.4 1.0
HG2 A:ARG58 3.3 5.7 1.0
CA A:LYS57 3.3 6.5 1.0
O A:PRO56 3.3 8.8 1.0
O A:ARG58 3.3 7.8 1.0
C A:LYS57 3.5 6.6 1.0
C A:TYR119 3.5 4.2 1.0
C A:ASN117 3.6 5.0 1.0
CB A:ASN117 3.7 7.1 1.0
HA A:ASN117 3.8 6.7 1.0
O A:HOH367 3.9 8.2 1.0
CA A:TRP120 3.9 4.4 1.0
CA A:ARG58 4.0 5.3 1.0
CE3 A:TRP120 4.0 6.2 1.0
CA A:ASN117 4.0 5.6 1.0
N A:TRP120 4.0 5.3 1.0
CG A:ARG58 4.0 4.8 1.0
C A:ARG58 4.1 6.4 1.0
C A:PRO56 4.1 7.4 1.0
HG3 A:ARG58 4.1 5.7 1.0
N A:LYS57 4.1 6.8 1.0
HB2 A:ASN117 4.2 8.6 1.0
HB2 A:TRP120 4.2 7.4 1.0
O A:HOH393 4.3 6.1 1.0
HB3 A:LYS57 4.3 9.1 1.0
HG2 A:LYS57 4.4 10.2 1.0
HD13 A:LEU63 4.4 8.8 1.0
CB A:LYS57 4.4 7.6 1.0
CB A:ARG58 4.5 5.0 1.0
N A:TYR119 4.5 4.5 1.0
HZ3 A:TRP120 4.5 7.0 1.0
HD11 A:LEU63 4.5 8.8 1.0
CB A:TRP120 4.6 6.2 1.0
H A:TYR119 4.6 5.3 1.0
CA A:TYR119 4.7 4.5 1.0
CZ3 A:TRP120 4.7 5.9 1.0
N A:TYR118 4.7 4.7 1.0
HB3 A:ARG58 4.7 6.1 1.0
C A:TYR118 4.7 4.6 1.0
H A:TRP120 4.7 6.3 1.0
O A:LYS57 4.7 7.2 1.0
HA A:ARG58 4.7 6.4 1.0
CD2 A:TRP120 4.8 4.8 1.0
CG A:ASN117 4.8 11.0 1.0
CD1 A:LEU63 4.8 7.3 1.0
H A:LYS57 4.9 8.1 1.0
CG A:LYS57 4.9 8.5 1.0
OD1 A:ASN117 4.9 13.8 1.0
HD12 A:LEU63 5.0 8.8 1.0

Sodium binding site 5 out of 8 in 7rjp

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Sodium binding site 5 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na206

b:16.1
occ:1.00
H A:VAL87 2.0 7.9 1.0
HA A:PRO86 2.8 7.6 1.0
N A:VAL87 2.8 6.6 1.0
O A:HOH380 2.9 6.6 1.0
HG23 A:VAL87 2.9 9.5 1.0
HB2 A:PRO104 3.0 6.8 1.0
NA A:NA207 3.1 14.4 1.0
HB A:VAL87 3.1 8.7 1.0
OH A:TYR98 3.1 7.9 1.0
HB3 A:PRO104 3.3 6.8 1.0
HH A:TYR98 3.4 9.5 1.0
HB3 A:PRO86 3.5 7.4 1.0
CA A:PRO86 3.5 6.3 1.0
CB A:PRO104 3.6 5.7 1.0
CB A:VAL87 3.6 7.2 1.0
HE2 A:TYR97 3.6 7.8 1.0
CG2 A:VAL87 3.6 7.9 1.0
C A:PRO86 3.7 6.6 1.0
CA A:VAL87 3.8 7.7 1.0
O A:HOH466 3.9 10.3 1.0
HE1 A:TYR98 3.9 8.1 1.0
H A:MET105 4.0 4.7 1.0
HG21 A:VAL87 4.0 9.5 1.0
HB3 A:ASP106 4.0 6.1 1.0
CB A:PRO86 4.0 6.2 1.0
CZ A:TYR98 4.2 6.5 1.0
O A:HOH343 4.2 7.2 1.0
HA A:PRO104 4.3 5.7 1.0
CE2 A:TYR97 4.3 6.5 1.0
OH A:TYR97 4.3 6.1 1.0
N A:MET105 4.4 3.9 1.0
CE1 A:TYR98 4.4 6.7 1.0
CA A:PRO104 4.4 4.8 1.0
HG22 A:VAL87 4.4 9.5 1.0
O A:VAL87 4.5 8.2 1.0
HA A:VAL87 4.5 9.3 1.0
O A:MET105 4.6 4.7 1.0
HB2 A:PRO86 4.6 7.4 1.0
C A:VAL87 4.6 7.9 1.0
C A:PRO104 4.7 4.0 1.0
CZ A:TYR97 4.7 6.1 1.0
O A:HOH364 4.8 6.9 1.0
OD1 A:ASP106 4.8 5.3 1.0
N A:PRO86 4.8 5.5 1.0
CG A:PRO104 4.8 5.7 1.0
O A:PRO86 4.9 7.0 1.0
C A:MET105 4.9 3.9 1.0
O A:GLN85 4.9 5.7 1.0
HG3 A:PRO104 4.9 6.9 1.0
HG3 A:PRO86 4.9 8.9 1.0
HH A:TYR97 4.9 7.3 1.0
CB A:ASP106 4.9 5.1 1.0

Sodium binding site 6 out of 8 in 7rjp

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Sodium binding site 6 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na207

b:14.4
occ:1.00
H A:MET105 2.4 4.7 1.0
HD22 A:ASN135 2.6 6.4 1.0
OH A:TYR97 2.7 6.1 1.0
HA A:PRO104 2.8 5.7 1.0
O A:HOH343 2.9 7.2 1.0
NA A:NA206 3.1 16.1 1.0
HH A:TYR97 3.1 7.3 1.0
O A:MET105 3.1 4.7 1.0
N A:MET105 3.2 3.9 1.0
ND2 A:ASN135 3.4 5.3 1.0
HG21 A:ILE101 3.5 7.6 1.0
CA A:PRO104 3.5 4.8 1.0
HB3 A:PRO104 3.6 6.8 1.0
HE2 A:TYR97 3.7 7.8 1.0
HB2 A:PRO104 3.7 6.8 1.0
HG23 A:VAL87 3.8 9.5 1.0
HD21 A:ASN135 3.8 6.4 1.0
HB3 A:ASN135 3.8 6.8 1.0
CB A:PRO104 3.8 5.7 1.0
C A:PRO104 3.9 4.0 1.0
CZ A:TYR97 3.9 6.1 1.0
HB2 A:ASN135 3.9 6.8 1.0
C A:MET105 3.9 3.9 1.0
O A:HOH349 4.0 7.3 1.0
O A:HOH326 4.1 6.2 1.0
CB A:ASN135 4.2 5.7 1.0
CE2 A:TYR97 4.2 6.5 1.0
CA A:MET105 4.2 3.9 1.0
HG21 A:VAL87 4.2 9.5 1.0
CG A:ASN135 4.2 4.7 1.0
CG2 A:ILE101 4.3 6.4 1.0
HG22 A:ILE101 4.3 7.6 1.0
HH33 B:ALY271 4.3 9.6 1.0
CG2 A:VAL87 4.4 7.9 1.0
HA A:MET132 4.5 3.7 1.0
O A:HOH380 4.5 6.6 1.0
H A:VAL87 4.6 7.9 1.0
HB3 A:ASP106 4.6 6.1 1.0
HG23 A:ILE101 4.7 7.6 1.0
HG3 A:MET132 4.7 5.2 1.0
HB A:VAL87 4.8 8.7 1.0
N A:PRO104 4.8 4.4 1.0
HA A:MET105 4.8 4.6 1.0
HB3 A:MET105 4.9 5.4 1.0
HG13 A:ILE101 5.0 7.7 1.0

Sodium binding site 7 out of 8 in 7rjp

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Sodium binding site 7 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na208

b:15.5
occ:1.00
O A:ARG68 2.8 8.1 1.0
CD A:LYS72 2.8 26.4 1.0
HB3 A:ARG68 2.8 8.4 1.0
HA A:ARG68 3.0 8.1 1.0
O A:HOH307 3.1 23.8 1.0
HD2 A:ARG68 3.1 10.6 1.0
CA A:ARG68 3.5 6.7 1.0
CB A:ARG68 3.5 7.0 1.0
C A:ARG68 3.6 6.3 1.0
HB2 A:LYS72 3.9 11.7 1.0
CD A:ARG68 3.9 8.8 1.0
CG A:LYS72 4.0 14.3 1.0
HD3 A:ARG68 4.0 10.6 1.0
HH11 A:ARG68 4.1 16.9 1.0
HB3 A:LYS72 4.2 11.7 1.0
CG A:ARG68 4.3 6.3 1.0
CB A:LYS72 4.3 9.8 1.0
HB2 A:ARG68 4.3 8.4 1.0
HG2 A:LYS72 4.3 17.1 1.0
O A:HOH436 4.6 13.8 1.0
HG3 A:ARG68 4.6 7.5 1.0
HG3 A:LYS72 4.8 17.1 1.0
N A:VAL69 4.9 6.0 1.0
NH1 A:ARG68 4.9 14.1 1.0
O A:HOH348 4.9 16.4 1.0
N A:ARG68 4.9 5.2 1.0

Sodium binding site 8 out of 8 in 7rjp

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Sodium binding site 8 out of 8 in the Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Crystal Structure of Human Bromodomain Containing Protein 4 (BRD4) in Complex with Shmt within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na209

b:24.4
occ:1.00
H A:GLN78 2.1 10.0 1.0
HG2 A:GLN78 2.7 22.0 1.0
HA A:HIS77 2.8 9.5 1.0
N A:GLN78 2.9 8.3 1.0
HB3 A:GLN78 3.2 15.3 1.0
CG A:GLN78 3.5 18.4 1.0
CA A:HIS77 3.6 7.9 1.0
CB A:GLN78 3.7 12.8 1.0
C A:HIS77 3.8 7.8 1.0
CG A:HIS77 3.8 9.5 1.0
CD2 A:HIS77 3.8 11.6 1.0
HZ3 A:LYS76 3.9 17.0 0.5
CA A:GLN78 3.9 8.8 1.0
ND1 A:HIS77 4.0 10.6 1.0
HE21 A:GLN78 4.0 40.1 1.0
NE2 A:HIS77 4.1 13.3 1.0
HD2 A:HIS77 4.1 13.9 1.0
CE1 A:HIS77 4.2 12.5 1.0
HG3 A:GLN78 4.2 22.0 1.0
CB A:HIS77 4.3 8.5 1.0
HA A:GLN78 4.4 10.5 1.0
CD A:GLN78 4.4 28.0 1.0
HE2 A:HIS77 4.5 15.9 1.0
NE2 A:GLN78 4.5 33.4 1.0
O A:LYS76 4.5 10.4 1.0
HB2 A:GLN78 4.6 15.3 1.0
HE1 A:HIS77 4.6 14.9 1.0
HD2 A:LYS76 4.7 23.9 0.5
H A:PHE79 4.7 9.3 1.0
NZ A:LYS76 4.7 14.2 0.5
HB2 A:HIS77 4.7 10.2 1.0
N A:HIS77 4.8 8.2 1.0
O A:HIS77 5.0 8.3 1.0

Reference:

S.Wagner, E.Fedorov, B.Sudhamalla, H.N.Jnawali, R.Debiec, A.Ghosh, K.Islam. Uncovering the Bromodomain Interactome Using Site-Specific Azide-Acetyllysine Photochemistry, Proteomic Profiling and Structural Characterization To Be Published.
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