Chlorine in PDB 8jgj: Cryo-Em Structure of Mclc-3 with Atp
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Cryo-Em Structure of Mclc-3 with Atp
(pdb code 8jgj). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
Cryo-Em Structure of Mclc-3 with Atp, PDB code: 8jgj:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 1 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl902
b:10.4
occ:1.00
|
HG13
|
A:ILE528
|
2.8
|
13.8
|
1.0
|
|
HB2
|
A:SER453
|
2.9
|
20.6
|
1.0
|
|
HG11
|
A:VAL273
|
3.1
|
11.8
|
1.0
|
|
HA2
|
A:GLY280
|
3.3
|
9.9
|
1.0
|
|
HG2
|
A:LYS281
|
3.3
|
12.5
|
1.0
|
|
H
|
A:LYS281
|
3.3
|
12.5
|
1.0
|
|
HG21
|
A:ILE528
|
3.4
|
13.8
|
1.0
|
|
OE2
|
A:GLU282
|
3.6
|
14.1
|
1.0
|
|
CG1
|
A:ILE528
|
3.8
|
13.8
|
1.0
|
|
HG3
|
A:LYS281
|
3.8
|
12.5
|
1.0
|
|
CB
|
A:SER453
|
3.8
|
20.6
|
1.0
|
|
CG1
|
A:VAL273
|
3.9
|
11.8
|
1.0
|
|
HG12
|
A:VAL273
|
3.9
|
11.8
|
1.0
|
|
CG
|
A:LYS281
|
4.0
|
12.5
|
1.0
|
|
HA3
|
A:GLY280
|
4.1
|
9.9
|
1.0
|
|
CA
|
A:GLY280
|
4.1
|
9.9
|
1.0
|
|
HB3
|
A:SER453
|
4.1
|
20.6
|
1.0
|
|
N
|
A:LYS281
|
4.1
|
12.5
|
1.0
|
|
H
|
A:SER453
|
4.1
|
20.6
|
1.0
|
|
HZ2
|
A:LYS281
|
4.1
|
12.5
|
1.0
|
|
HE3
|
A:LYS281
|
4.2
|
12.5
|
1.0
|
|
HD11
|
A:ILE528
|
4.2
|
13.8
|
1.0
|
|
HG12
|
A:ILE528
|
4.2
|
13.8
|
1.0
|
|
CG2
|
A:ILE528
|
4.3
|
13.8
|
1.0
|
|
HD22
|
A:ASN451
|
4.3
|
21.0
|
1.0
|
|
HG13
|
A:VAL273
|
4.3
|
11.8
|
1.0
|
|
HG22
|
A:VAL273
|
4.3
|
11.8
|
1.0
|
|
HG
|
A:SER453
|
4.3
|
20.6
|
1.0
|
|
HG2
|
A:GLU282
|
4.4
|
14.1
|
1.0
|
|
HB
|
A:ILE528
|
4.4
|
13.8
|
1.0
|
|
CB
|
A:ILE528
|
4.4
|
13.8
|
1.0
|
|
CD1
|
A:ILE528
|
4.5
|
13.8
|
1.0
|
|
OG
|
A:SER453
|
4.6
|
20.6
|
1.0
|
|
HG21
|
A:VAL273
|
4.6
|
11.8
|
1.0
|
|
C
|
A:GLY280
|
4.6
|
9.9
|
1.0
|
|
HD12
|
A:ILE528
|
4.6
|
13.8
|
1.0
|
|
N
|
A:SER453
|
4.6
|
20.6
|
1.0
|
|
HB
|
A:THR452
|
4.6
|
16.6
|
1.0
|
|
CD
|
A:GLU282
|
4.7
|
14.1
|
1.0
|
|
O
|
A:LEU279
|
4.7
|
9.5
|
1.0
|
|
HG22
|
A:ILE528
|
4.7
|
13.8
|
1.0
|
|
CA
|
A:SER453
|
4.8
|
20.6
|
1.0
|
|
CG2
|
A:VAL273
|
4.8
|
11.8
|
1.0
|
|
CE
|
A:LYS281
|
4.8
|
12.5
|
1.0
|
|
HG23
|
A:ILE528
|
4.9
|
13.8
|
1.0
|
|
NZ
|
A:LYS281
|
4.9
|
12.5
|
1.0
|
|
CD
|
A:LYS281
|
5.0
|
12.5
|
1.0
|
|
CB
|
A:VAL273
|
5.0
|
11.8
|
1.0
|
|
HA
|
A:SER453
|
5.0
|
20.6
|
1.0
|
|
CG
|
A:GLU282
|
5.0
|
14.1
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 2 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl903
b:22.0
occ:1.00
|
HA3
|
A:GLY238
|
3.1
|
9.3
|
1.0
|
|
HA2
|
A:GLY519
|
3.2
|
12.5
|
1.0
|
|
HA2
|
A:GLY238
|
3.5
|
9.3
|
1.0
|
|
CA
|
A:GLY238
|
3.7
|
9.3
|
1.0
|
|
HA3
|
A:GLY519
|
3.9
|
12.5
|
1.0
|
|
H
|
A:SER239
|
4.0
|
9.1
|
1.0
|
|
CA
|
A:GLY519
|
4.0
|
12.5
|
1.0
|
|
ND1
|
A:HIS633
|
4.4
|
9.1
|
1.0
|
|
N
|
A:SER239
|
4.6
|
9.1
|
1.0
|
|
CE1
|
A:HIS633
|
4.6
|
9.1
|
1.0
|
|
HD22
|
A:ASN637
|
4.6
|
11.2
|
1.0
|
|
N
|
A:GLY238
|
4.7
|
9.3
|
1.0
|
|
C
|
A:GLY238
|
4.7
|
9.3
|
1.0
|
|
O
|
A:PHE518
|
4.8
|
9.3
|
1.0
|
|
N
|
A:GLY519
|
4.8
|
12.5
|
1.0
|
|
H
|
A:ILE520
|
4.9
|
11.5
|
1.0
|
|
H
|
A:GLY240
|
4.9
|
10.2
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 3 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl904
b:9.8
occ:1.00
|
OG
|
A:SER239
|
2.4
|
9.1
|
1.0
|
|
HG
|
A:SER239
|
2.5
|
9.1
|
1.0
|
|
OH
|
A:TYR630
|
2.6
|
11.8
|
1.0
|
|
H
|
A:LEU526
|
2.6
|
10.7
|
1.0
|
|
HD12
|
A:ILE241
|
2.7
|
11.6
|
1.0
|
|
HB2
|
A:SER239
|
2.9
|
9.1
|
1.0
|
|
HE1
|
A:TYR630
|
2.9
|
11.8
|
1.0
|
|
CB
|
A:SER239
|
3.1
|
9.1
|
1.0
|
|
HA3
|
A:GLY283
|
3.1
|
10.9
|
1.0
|
|
HH
|
A:TYR630
|
3.2
|
11.8
|
1.0
|
|
CZ
|
A:TYR630
|
3.4
|
11.8
|
1.0
|
|
HB3
|
A:LEU526
|
3.4
|
10.7
|
1.0
|
|
CE1
|
A:TYR630
|
3.4
|
11.8
|
1.0
|
|
HB3
|
A:SER239
|
3.4
|
9.1
|
1.0
|
|
N
|
A:LEU526
|
3.4
|
10.7
|
1.0
|
|
HA2
|
A:GLY525
|
3.5
|
8.7
|
1.0
|
|
CD1
|
A:ILE241
|
3.6
|
11.6
|
1.0
|
|
HD11
|
A:ILE241
|
3.7
|
11.6
|
1.0
|
|
HB2
|
A:LEU526
|
3.8
|
10.7
|
1.0
|
|
HA2
|
A:GLY283
|
3.9
|
10.9
|
1.0
|
|
CA
|
A:GLY283
|
3.9
|
10.9
|
1.0
|
|
HZ
|
A:PHE518
|
3.9
|
9.3
|
1.0
|
|
CB
|
A:LEU526
|
4.0
|
10.7
|
1.0
|
|
HB
|
A:ILE241
|
4.0
|
11.6
|
1.0
|
|
H
|
A:PHE527
|
4.1
|
12.8
|
1.0
|
|
CA
|
A:GLY525
|
4.2
|
8.7
|
1.0
|
|
HD13
|
A:ILE241
|
4.2
|
11.6
|
1.0
|
|
HE1
|
A:PHE518
|
4.2
|
9.3
|
1.0
|
|
CA
|
A:LEU526
|
4.2
|
10.7
|
1.0
|
|
HA3
|
A:GLY525
|
4.3
|
8.7
|
1.0
|
|
C
|
A:GLY525
|
4.3
|
8.7
|
1.0
|
|
HG13
|
A:ILE241
|
4.3
|
11.6
|
1.0
|
|
HD3
|
A:PRO284
|
4.4
|
9.8
|
1.0
|
|
CG1
|
A:ILE241
|
4.4
|
11.6
|
1.0
|
|
CA
|
A:SER239
|
4.5
|
9.1
|
1.0
|
|
CZ
|
A:PHE518
|
4.5
|
9.3
|
1.0
|
|
C
|
A:GLY283
|
4.6
|
10.9
|
1.0
|
|
N
|
A:PHE527
|
4.6
|
12.8
|
1.0
|
|
CE2
|
A:PHE527
|
4.6
|
12.8
|
1.0
|
|
HA
|
A:SER239
|
4.6
|
9.1
|
1.0
|
|
CE2
|
A:TYR630
|
4.6
|
11.8
|
1.0
|
|
CD2
|
A:PHE527
|
4.6
|
12.8
|
1.0
|
|
CE1
|
A:PHE518
|
4.7
|
9.3
|
1.0
|
|
CD1
|
A:TYR630
|
4.7
|
11.8
|
1.0
|
|
HE2
|
A:PHE527
|
4.7
|
12.8
|
1.0
|
|
CB
|
A:ILE241
|
4.7
|
11.6
|
1.0
|
|
HD2
|
A:PHE527
|
4.7
|
12.8
|
1.0
|
|
C
|
A:LEU526
|
4.7
|
10.7
|
1.0
|
|
H
|
A:ILE241
|
4.8
|
11.6
|
1.0
|
|
HE2
|
A:TYR630
|
4.9
|
11.8
|
1.0
|
|
O
|
A:GLY283
|
5.0
|
10.9
|
1.0
|
|
HD3
|
A:PRO242
|
5.0
|
10.5
|
1.0
|
|
H
|
A:GLY283
|
5.0
|
10.9
|
1.0
|
|
CZ
|
A:PHE527
|
5.0
|
12.8
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 4 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl902
b:9.5
occ:1.00
|
HG13
|
B:ILE528
|
2.8
|
13.6
|
1.0
|
|
HB2
|
B:SER453
|
3.0
|
20.2
|
1.0
|
|
HG11
|
B:VAL273
|
3.0
|
11.5
|
1.0
|
|
HA2
|
B:GLY280
|
3.3
|
9.8
|
1.0
|
|
HG21
|
B:ILE528
|
3.3
|
13.6
|
1.0
|
|
H
|
B:LYS281
|
3.3
|
12.1
|
1.0
|
|
HG2
|
B:LYS281
|
3.3
|
12.1
|
1.0
|
|
CG1
|
B:ILE528
|
3.8
|
13.6
|
1.0
|
|
OE2
|
B:GLU282
|
3.8
|
13.7
|
1.0
|
|
HG3
|
B:LYS281
|
3.8
|
12.1
|
1.0
|
|
CG1
|
B:VAL273
|
3.9
|
11.5
|
1.0
|
|
HG12
|
B:VAL273
|
3.9
|
11.5
|
1.0
|
|
CB
|
B:SER453
|
3.9
|
20.2
|
1.0
|
|
HA3
|
B:GLY280
|
4.0
|
9.8
|
1.0
|
|
CG
|
B:LYS281
|
4.0
|
12.1
|
1.0
|
|
CA
|
B:GLY280
|
4.0
|
9.8
|
1.0
|
|
N
|
B:LYS281
|
4.1
|
12.1
|
1.0
|
|
HB3
|
B:SER453
|
4.1
|
20.2
|
1.0
|
|
H
|
B:SER453
|
4.1
|
20.2
|
1.0
|
|
CG2
|
B:ILE528
|
4.2
|
13.6
|
1.0
|
|
HE3
|
B:LYS281
|
4.2
|
12.1
|
1.0
|
|
HG2
|
B:GLU282
|
4.2
|
13.7
|
1.0
|
|
HZ2
|
B:LYS281
|
4.2
|
12.1
|
1.0
|
|
HG12
|
B:ILE528
|
4.3
|
13.6
|
1.0
|
|
HD11
|
B:ILE528
|
4.3
|
13.6
|
1.0
|
|
HG13
|
B:VAL273
|
4.3
|
11.5
|
1.0
|
|
HG22
|
B:VAL273
|
4.3
|
11.5
|
1.0
|
|
HD22
|
B:ASN451
|
4.3
|
20.7
|
1.0
|
|
HB
|
B:ILE528
|
4.3
|
13.6
|
1.0
|
|
CB
|
B:ILE528
|
4.4
|
13.6
|
1.0
|
|
HG
|
B:SER453
|
4.4
|
20.2
|
1.0
|
|
CD1
|
B:ILE528
|
4.5
|
13.6
|
1.0
|
|
HG21
|
B:VAL273
|
4.6
|
11.5
|
1.0
|
|
OG
|
B:SER453
|
4.6
|
20.2
|
1.0
|
|
HG22
|
B:ILE528
|
4.6
|
13.6
|
1.0
|
|
C
|
B:GLY280
|
4.6
|
9.8
|
1.0
|
|
N
|
B:SER453
|
4.7
|
20.2
|
1.0
|
|
HD12
|
B:ILE528
|
4.7
|
13.6
|
1.0
|
|
HB
|
B:THR452
|
4.7
|
16.4
|
1.0
|
|
O
|
B:LEU279
|
4.7
|
9.4
|
1.0
|
|
CD
|
B:GLU282
|
4.8
|
13.7
|
1.0
|
|
HG23
|
B:ILE528
|
4.8
|
13.6
|
1.0
|
|
CG2
|
B:VAL273
|
4.8
|
11.5
|
1.0
|
|
CA
|
B:SER453
|
4.8
|
20.2
|
1.0
|
|
CE
|
B:LYS281
|
4.9
|
12.1
|
1.0
|
|
CG
|
B:GLU282
|
4.9
|
13.7
|
1.0
|
|
CB
|
B:VAL273
|
5.0
|
11.5
|
1.0
|
|
NZ
|
B:LYS281
|
5.0
|
12.1
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 5 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl903
b:22.0
occ:1.00
|
HA3
|
B:GLY238
|
3.1
|
9.6
|
1.0
|
|
HA2
|
B:GLY519
|
3.2
|
12.3
|
1.0
|
|
HA2
|
B:GLY238
|
3.5
|
9.6
|
1.0
|
|
CA
|
B:GLY238
|
3.7
|
9.6
|
1.0
|
|
HA3
|
B:GLY519
|
3.9
|
12.3
|
1.0
|
|
H
|
B:SER239
|
4.0
|
9.2
|
1.0
|
|
CA
|
B:GLY519
|
4.0
|
12.3
|
1.0
|
|
ND1
|
B:HIS633
|
4.4
|
8.9
|
1.0
|
|
N
|
B:SER239
|
4.6
|
9.2
|
1.0
|
|
CE1
|
B:HIS633
|
4.6
|
8.9
|
1.0
|
|
HD22
|
B:ASN637
|
4.6
|
11.1
|
1.0
|
|
N
|
B:GLY238
|
4.7
|
9.6
|
1.0
|
|
C
|
B:GLY238
|
4.7
|
9.6
|
1.0
|
|
O
|
B:PHE518
|
4.8
|
9.4
|
1.0
|
|
N
|
B:GLY519
|
4.8
|
12.3
|
1.0
|
|
H
|
B:ILE520
|
4.9
|
11.4
|
1.0
|
|
H
|
B:GLY240
|
4.9
|
10.1
|
1.0
|
|
Chlorine binding site 6 out
of 6 in 8jgj
Go back to
Chlorine Binding Sites List in 8jgj
Chlorine binding site 6 out
of 6 in the Cryo-Em Structure of Mclc-3 with Atp
 Mono view
 Stereo pair view
|
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Cryo-Em Structure of Mclc-3 with Atp within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl904
b:10.4
occ:1.00
|
OG
|
B:SER239
|
2.4
|
9.2
|
1.0
|
|
HG
|
B:SER239
|
2.5
|
9.2
|
1.0
|
|
OH
|
B:TYR630
|
2.6
|
11.9
|
1.0
|
|
H
|
B:LEU526
|
2.6
|
10.8
|
1.0
|
|
HD12
|
B:ILE241
|
2.7
|
11.5
|
1.0
|
|
HB2
|
B:SER239
|
2.9
|
9.2
|
1.0
|
|
HE1
|
B:TYR630
|
2.9
|
11.9
|
1.0
|
|
HA3
|
B:GLY283
|
3.1
|
10.9
|
1.0
|
|
CB
|
B:SER239
|
3.1
|
9.2
|
1.0
|
|
HH
|
B:TYR630
|
3.2
|
11.9
|
1.0
|
|
CZ
|
B:TYR630
|
3.4
|
11.9
|
1.0
|
|
HB3
|
B:LEU526
|
3.4
|
10.8
|
1.0
|
|
CE1
|
B:TYR630
|
3.4
|
11.9
|
1.0
|
|
HB3
|
B:SER239
|
3.4
|
9.2
|
1.0
|
|
N
|
B:LEU526
|
3.4
|
10.8
|
1.0
|
|
HA2
|
B:GLY525
|
3.5
|
8.9
|
1.0
|
|
CD1
|
B:ILE241
|
3.6
|
11.5
|
1.0
|
|
HD11
|
B:ILE241
|
3.7
|
11.5
|
1.0
|
|
HB2
|
B:LEU526
|
3.8
|
10.8
|
1.0
|
|
CA
|
B:GLY283
|
3.9
|
10.9
|
1.0
|
|
HZ
|
B:PHE518
|
3.9
|
9.4
|
1.0
|
|
HA2
|
B:GLY283
|
3.9
|
10.9
|
1.0
|
|
HB
|
B:ILE241
|
4.0
|
11.5
|
1.0
|
|
CB
|
B:LEU526
|
4.0
|
10.8
|
1.0
|
|
H
|
B:PHE527
|
4.1
|
12.8
|
1.0
|
|
CA
|
B:GLY525
|
4.2
|
8.9
|
1.0
|
|
HE1
|
B:PHE518
|
4.2
|
9.4
|
1.0
|
|
HD13
|
B:ILE241
|
4.2
|
11.5
|
1.0
|
|
CA
|
B:LEU526
|
4.2
|
10.8
|
1.0
|
|
HD3
|
B:PRO284
|
4.3
|
9.9
|
1.0
|
|
C
|
B:GLY525
|
4.3
|
8.9
|
1.0
|
|
HG13
|
B:ILE241
|
4.3
|
11.5
|
1.0
|
|
HA3
|
B:GLY525
|
4.3
|
8.9
|
1.0
|
|
CG1
|
B:ILE241
|
4.4
|
11.5
|
1.0
|
|
CA
|
B:SER239
|
4.5
|
9.2
|
1.0
|
|
CZ
|
B:PHE518
|
4.5
|
9.4
|
1.0
|
|
C
|
B:GLY283
|
4.5
|
10.9
|
1.0
|
|
N
|
B:PHE527
|
4.6
|
12.8
|
1.0
|
|
HA
|
B:SER239
|
4.6
|
9.2
|
1.0
|
|
CE2
|
B:TYR630
|
4.6
|
11.9
|
1.0
|
|
CE2
|
B:PHE527
|
4.6
|
12.8
|
1.0
|
|
CE1
|
B:PHE518
|
4.6
|
9.4
|
1.0
|
|
CD2
|
B:PHE527
|
4.7
|
12.8
|
1.0
|
|
CD1
|
B:TYR630
|
4.7
|
11.9
|
1.0
|
|
CB
|
B:ILE241
|
4.7
|
11.5
|
1.0
|
|
HE2
|
B:PHE527
|
4.7
|
12.8
|
1.0
|
|
HD2
|
B:PHE527
|
4.7
|
12.8
|
1.0
|
|
C
|
B:LEU526
|
4.8
|
10.8
|
1.0
|
|
H
|
B:ILE241
|
4.8
|
11.5
|
1.0
|
|
H
|
B:GLY283
|
4.9
|
10.9
|
1.0
|
|
HE2
|
B:TYR630
|
4.9
|
11.9
|
1.0
|
|
O
|
B:GLY283
|
4.9
|
10.9
|
1.0
|
|
N
|
B:GLY283
|
5.0
|
10.9
|
1.0
|
|
HD3
|
B:PRO242
|
5.0
|
10.3
|
1.0
|
|
Reference:
Y.Wan,
S.Guo,
W.Zhen,
L.Xu,
X.Chen,
F.Liu,
Y.Shen,
S.Liu,
L.Hu,
X.Wang,
F.Ye,
Q.Wang,
H.Wen,
F.Yang.
Structural Basis of Adenine Nucleotides Regulation and Neurodegenerative Pathology in Clc-3 Exchanger. Nat Commun V. 15 6654 2024.
ISSN: ESSN 2041-1723
PubMed: 39107281
DOI: 10.1038/S41467-024-50975-W
Page generated: Sat Sep 28 19:24:42 2024
|
