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:
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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
Go back to
Sodium Binding Sites List in 7rjp
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.
Page generated: Wed Oct 9 08:34:47 2024
|
