Zinc in PDB 1u10: Mepa, Active Form with Zn in P1
Protein crystallography data
The structure of Mepa, Active Form with Zn in P1, PDB code: 1u10
was solved by
M.Marcyjaniak,
S.G.Odintsov,
I.Sabala,
M.Bochtler,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.40
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
35.613,
77.988,
127.663,
93.15,
95.93,
90.75
|
R / Rfree (%)
|
23.4 /
26.6
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Mepa, Active Form with Zn in P1
(pdb code 1u10). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the
Mepa, Active Form with Zn in P1, PDB code: 1u10:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Zinc binding site 1 out
of 9 in 1u10
Go back to
Zinc Binding Sites List in 1u10
Zinc binding site 1 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn400
b:25.9
occ:1.00
|
ND1
|
A:HIS110
|
2.0
|
29.9
|
1.0
|
ND1
|
A:HIS211
|
2.0
|
17.4
|
1.0
|
NE2
|
A:HIS113
|
2.0
|
29.0
|
1.0
|
OD1
|
A:ASP120
|
2.1
|
18.5
|
1.0
|
CE1
|
A:HIS211
|
2.6
|
18.7
|
1.0
|
CG
|
A:ASP120
|
2.8
|
19.6
|
1.0
|
OD2
|
A:ASP120
|
2.8
|
21.7
|
1.0
|
CE1
|
A:HIS110
|
2.8
|
29.3
|
1.0
|
CE1
|
A:HIS113
|
2.9
|
28.8
|
1.0
|
CD2
|
A:HIS113
|
3.1
|
26.9
|
1.0
|
CG
|
A:HIS110
|
3.1
|
31.5
|
1.0
|
CG
|
A:HIS211
|
3.3
|
20.2
|
1.0
|
CB
|
A:HIS110
|
3.6
|
32.4
|
1.0
|
NE2
|
A:HIS211
|
3.8
|
20.0
|
1.0
|
CB
|
A:HIS211
|
4.0
|
20.4
|
1.0
|
NE2
|
A:HIS110
|
4.0
|
30.5
|
1.0
|
ND1
|
A:HIS113
|
4.1
|
26.5
|
1.0
|
CD2
|
A:HIS110
|
4.2
|
30.1
|
1.0
|
CD2
|
A:HIS211
|
4.2
|
18.5
|
1.0
|
CG
|
A:HIS113
|
4.2
|
25.8
|
1.0
|
CB
|
A:ASP120
|
4.2
|
18.5
|
1.0
|
CA
|
A:HIS211
|
4.6
|
22.2
|
1.0
|
CA
|
A:ASP120
|
4.8
|
18.7
|
1.0
|
N
|
A:ASP120
|
4.8
|
17.4
|
1.0
|
NE2
|
A:HIS206
|
4.8
|
28.8
|
1.0
|
|
Zinc binding site 2 out
of 9 in 1u10
Go back to
Zinc Binding Sites List in 1u10
Zinc binding site 2 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn601
b:49.4
occ:1.00
|
OD2
|
A:ASP147
|
1.9
|
42.5
|
1.0
|
NE2
|
A:HIS150
|
2.0
|
32.4
|
1.0
|
NE2
|
B:HIS150
|
2.0
|
35.4
|
1.0
|
OD2
|
B:ASP147
|
2.3
|
42.1
|
1.0
|
CD2
|
A:HIS150
|
2.6
|
30.9
|
1.0
|
CD2
|
B:HIS150
|
2.8
|
35.7
|
1.0
|
CG
|
A:ASP147
|
2.9
|
41.0
|
1.0
|
CE1
|
B:HIS150
|
3.1
|
35.1
|
1.0
|
OD1
|
A:ASP147
|
3.2
|
39.6
|
1.0
|
CE1
|
A:HIS150
|
3.3
|
31.6
|
1.0
|
CG
|
B:ASP147
|
3.4
|
43.0
|
1.0
|
OD1
|
B:ASP147
|
3.9
|
40.9
|
1.0
|
CG
|
A:HIS150
|
3.9
|
32.6
|
1.0
|
CG
|
B:HIS150
|
4.0
|
36.7
|
1.0
|
CB
|
A:LYS149
|
4.1
|
38.4
|
1.0
|
ND1
|
B:HIS150
|
4.1
|
36.6
|
1.0
|
ND1
|
A:HIS150
|
4.2
|
32.2
|
1.0
|
CB
|
A:ASP147
|
4.2
|
39.5
|
1.0
|
CG
|
A:LYS149
|
4.3
|
41.8
|
1.0
|
CG
|
B:LYS149
|
4.4
|
40.0
|
1.0
|
CB
|
B:LYS149
|
4.4
|
37.6
|
1.0
|
CB
|
B:ASP147
|
4.6
|
42.7
|
1.0
|
OG
|
A:SER145
|
4.7
|
39.4
|
1.0
|
CA
|
A:LYS149
|
4.9
|
36.7
|
1.0
|
N
|
A:LYS149
|
4.9
|
35.3
|
1.0
|
|
Zinc binding site 3 out
of 9 in 1u10
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Zinc Binding Sites List in 1u10
Zinc binding site 3 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn400
b:15.9
occ:1.00
|
ND1
|
B:HIS110
|
2.0
|
28.1
|
1.0
|
NE2
|
B:HIS113
|
2.0
|
11.7
|
1.0
|
ND1
|
B:HIS211
|
2.0
|
15.4
|
1.0
|
OD1
|
B:ASP120
|
2.1
|
13.1
|
1.0
|
CE1
|
B:HIS211
|
2.7
|
19.4
|
1.0
|
CG
|
B:ASP120
|
2.8
|
12.5
|
1.0
|
OD2
|
B:ASP120
|
2.8
|
12.4
|
1.0
|
CE1
|
B:HIS110
|
2.9
|
29.1
|
1.0
|
CE1
|
B:HIS113
|
3.0
|
11.3
|
1.0
|
CD2
|
B:HIS113
|
3.1
|
11.1
|
1.0
|
CG
|
B:HIS110
|
3.1
|
27.2
|
1.0
|
CG
|
B:HIS211
|
3.3
|
17.0
|
1.0
|
CB
|
B:HIS110
|
3.5
|
26.0
|
1.0
|
CB
|
B:HIS211
|
3.9
|
14.4
|
1.0
|
NE2
|
B:HIS211
|
3.9
|
18.2
|
1.0
|
NE2
|
B:HIS110
|
4.1
|
29.5
|
1.0
|
ND1
|
B:HIS113
|
4.1
|
11.8
|
1.0
|
CD2
|
B:HIS110
|
4.2
|
27.9
|
1.0
|
CG
|
B:HIS113
|
4.2
|
12.2
|
1.0
|
CB
|
B:ASP120
|
4.2
|
10.2
|
1.0
|
CD2
|
B:HIS211
|
4.2
|
17.0
|
1.0
|
CA
|
B:HIS211
|
4.6
|
15.3
|
1.0
|
CA
|
B:ASP120
|
4.7
|
10.0
|
1.0
|
N
|
B:ASP120
|
4.8
|
10.3
|
1.0
|
NE2
|
B:HIS206
|
4.8
|
25.8
|
1.0
|
CA
|
B:HIS110
|
5.0
|
25.4
|
1.0
|
|
Zinc binding site 4 out
of 9 in 1u10
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Zinc Binding Sites List in 1u10
Zinc binding site 4 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Zn400
b:15.0
occ:1.00
|
ND1
|
C:HIS110
|
2.0
|
24.7
|
1.0
|
OD1
|
C:ASP120
|
2.0
|
7.0
|
1.0
|
NE2
|
C:HIS113
|
2.0
|
8.9
|
1.0
|
ND1
|
C:HIS211
|
2.1
|
15.1
|
1.0
|
CE1
|
C:HIS211
|
2.7
|
16.7
|
1.0
|
CG
|
C:ASP120
|
2.8
|
11.2
|
1.0
|
CE1
|
C:HIS110
|
2.8
|
26.6
|
1.0
|
OD2
|
C:ASP120
|
2.9
|
8.6
|
1.0
|
CE1
|
C:HIS113
|
3.0
|
13.0
|
1.0
|
CD2
|
C:HIS113
|
3.0
|
11.0
|
1.0
|
CG
|
C:HIS110
|
3.1
|
25.6
|
1.0
|
CG
|
C:HIS211
|
3.4
|
14.9
|
1.0
|
CB
|
C:HIS110
|
3.5
|
25.2
|
1.0
|
NE2
|
C:HIS211
|
3.9
|
18.2
|
1.0
|
NE2
|
C:HIS110
|
4.0
|
26.1
|
1.0
|
CB
|
C:HIS211
|
4.0
|
14.1
|
1.0
|
ND1
|
C:HIS113
|
4.1
|
10.1
|
1.0
|
CG
|
C:HIS113
|
4.2
|
11.8
|
1.0
|
CD2
|
C:HIS110
|
4.2
|
25.1
|
1.0
|
CB
|
C:ASP120
|
4.2
|
10.3
|
1.0
|
CD2
|
C:HIS211
|
4.3
|
15.4
|
1.0
|
NE2
|
C:HIS209
|
4.7
|
33.5
|
1.0
|
CA
|
C:ASP120
|
4.7
|
9.9
|
1.0
|
N
|
C:ASP120
|
4.7
|
7.8
|
1.0
|
CA
|
C:HIS211
|
4.8
|
15.2
|
1.0
|
NE2
|
C:HIS206
|
4.9
|
27.1
|
1.0
|
OG
|
C:SER112
|
4.9
|
20.6
|
1.0
|
|
Zinc binding site 5 out
of 9 in 1u10
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Zinc Binding Sites List in 1u10
Zinc binding site 5 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn400
b:11.8
occ:1.00
|
OD1
|
D:ASP120
|
1.9
|
8.9
|
1.0
|
ND1
|
D:HIS110
|
2.0
|
16.5
|
1.0
|
NE2
|
D:HIS113
|
2.0
|
10.9
|
1.0
|
ND1
|
D:HIS211
|
2.0
|
15.2
|
1.0
|
CG
|
D:ASP120
|
2.7
|
9.3
|
1.0
|
CE1
|
D:HIS211
|
2.8
|
14.2
|
1.0
|
OD2
|
D:ASP120
|
2.8
|
10.1
|
1.0
|
CE1
|
D:HIS110
|
2.9
|
17.6
|
1.0
|
CE1
|
D:HIS113
|
2.9
|
10.7
|
1.0
|
CG
|
D:HIS110
|
3.0
|
19.6
|
1.0
|
CD2
|
D:HIS113
|
3.1
|
8.6
|
1.0
|
CG
|
D:HIS211
|
3.2
|
14.2
|
1.0
|
CB
|
D:HIS110
|
3.5
|
20.6
|
1.0
|
CB
|
D:HIS211
|
3.8
|
11.8
|
1.0
|
NE2
|
D:HIS211
|
4.0
|
13.1
|
1.0
|
NE2
|
D:HIS110
|
4.0
|
20.3
|
1.0
|
ND1
|
D:HIS113
|
4.1
|
8.5
|
1.0
|
CB
|
D:ASP120
|
4.1
|
8.5
|
1.0
|
CD2
|
D:HIS110
|
4.1
|
19.5
|
1.0
|
O
|
D:HOH607
|
4.2
|
28.4
|
1.0
|
CG
|
D:HIS113
|
4.2
|
8.2
|
1.0
|
CD2
|
D:HIS211
|
4.2
|
12.5
|
1.0
|
NE2
|
D:HIS206
|
4.5
|
24.8
|
1.0
|
CA
|
D:HIS211
|
4.6
|
13.0
|
1.0
|
CA
|
D:ASP120
|
4.6
|
9.8
|
1.0
|
N
|
D:ASP120
|
4.7
|
10.7
|
1.0
|
CA
|
D:HIS110
|
4.9
|
21.9
|
1.0
|
|
Zinc binding site 6 out
of 9 in 1u10
Go back to
Zinc Binding Sites List in 1u10
Zinc binding site 6 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Zn602
b:27.9
occ:1.00
|
NE2
|
D:HIS150
|
2.0
|
31.4
|
1.0
|
NE2
|
C:HIS150
|
2.0
|
31.4
|
1.0
|
OD2
|
D:ASP147
|
2.1
|
39.9
|
1.0
|
OD2
|
C:ASP147
|
2.1
|
44.0
|
1.0
|
CD2
|
C:HIS150
|
2.8
|
31.2
|
1.0
|
CD2
|
D:HIS150
|
2.9
|
30.6
|
1.0
|
CG
|
D:ASP147
|
3.1
|
39.7
|
1.0
|
CE1
|
D:HIS150
|
3.1
|
32.4
|
1.0
|
CE1
|
C:HIS150
|
3.2
|
32.5
|
1.0
|
CG
|
C:ASP147
|
3.3
|
44.2
|
1.0
|
OD1
|
D:ASP147
|
3.5
|
37.8
|
1.0
|
OD1
|
C:ASP147
|
3.7
|
44.5
|
1.0
|
CG
|
C:HIS150
|
4.0
|
32.8
|
1.0
|
CG
|
D:HIS150
|
4.1
|
31.8
|
1.0
|
ND1
|
D:HIS150
|
4.2
|
31.8
|
1.0
|
ND1
|
C:HIS150
|
4.2
|
32.4
|
1.0
|
CB
|
C:LYS149
|
4.2
|
40.6
|
1.0
|
CB
|
D:ASP147
|
4.4
|
38.9
|
1.0
|
CB
|
C:ASP147
|
4.5
|
43.7
|
1.0
|
CG
|
C:LYS149
|
4.6
|
43.6
|
1.0
|
CB
|
D:LYS149
|
4.6
|
33.8
|
1.0
|
CG
|
D:LYS149
|
5.0
|
37.0
|
1.0
|
|
Zinc binding site 7 out
of 9 in 1u10
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Zinc Binding Sites List in 1u10
Zinc binding site 7 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn400
b:16.4
occ:1.00
|
ND1
|
E:HIS110
|
2.0
|
19.7
|
1.0
|
OD1
|
E:ASP120
|
2.0
|
9.9
|
1.0
|
NE2
|
E:HIS113
|
2.0
|
12.6
|
1.0
|
ND1
|
E:HIS211
|
2.0
|
15.3
|
1.0
|
CG
|
E:ASP120
|
2.7
|
10.7
|
1.0
|
CE1
|
E:HIS211
|
2.8
|
14.4
|
1.0
|
CE1
|
E:HIS110
|
2.8
|
21.3
|
1.0
|
OD2
|
E:ASP120
|
2.9
|
7.2
|
1.0
|
CE1
|
E:HIS113
|
3.0
|
12.1
|
1.0
|
CD2
|
E:HIS113
|
3.0
|
12.5
|
1.0
|
CG
|
E:HIS110
|
3.1
|
19.2
|
1.0
|
CG
|
E:HIS211
|
3.2
|
13.6
|
1.0
|
CB
|
E:HIS110
|
3.6
|
17.4
|
1.0
|
CB
|
E:HIS211
|
3.8
|
12.7
|
1.0
|
NE2
|
E:HIS211
|
4.0
|
15.0
|
1.0
|
NE2
|
E:HIS110
|
4.0
|
20.4
|
1.0
|
ND1
|
E:HIS113
|
4.1
|
12.6
|
1.0
|
CG
|
E:HIS113
|
4.2
|
12.4
|
1.0
|
CD2
|
E:HIS110
|
4.2
|
18.7
|
1.0
|
CB
|
E:ASP120
|
4.2
|
10.5
|
1.0
|
CD2
|
E:HIS211
|
4.2
|
13.1
|
1.0
|
CA
|
E:HIS211
|
4.5
|
14.2
|
1.0
|
CA
|
E:ASP120
|
4.7
|
10.8
|
1.0
|
NE2
|
E:HIS206
|
4.7
|
23.0
|
1.0
|
N
|
E:ASP120
|
4.7
|
9.7
|
1.0
|
|
Zinc binding site 8 out
of 9 in 1u10
Go back to
Zinc Binding Sites List in 1u10
Zinc binding site 8 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Zn603
b:33.1
occ:1.00
|
NE2
|
E:HIS150
|
2.0
|
32.4
|
1.0
|
NE2
|
F:HIS150
|
2.0
|
29.9
|
1.0
|
OD2
|
E:ASP147
|
2.0
|
35.0
|
1.0
|
OD2
|
F:ASP147
|
2.1
|
39.1
|
1.0
|
CE1
|
E:HIS150
|
2.5
|
31.6
|
1.0
|
CD2
|
F:HIS150
|
2.9
|
30.3
|
1.0
|
CG
|
E:ASP147
|
2.9
|
38.5
|
1.0
|
CE1
|
F:HIS150
|
3.1
|
29.1
|
1.0
|
CG
|
F:ASP147
|
3.2
|
40.5
|
1.0
|
OD1
|
E:ASP147
|
3.2
|
40.6
|
1.0
|
CD2
|
E:HIS150
|
3.3
|
30.9
|
1.0
|
OD1
|
F:ASP147
|
3.6
|
42.1
|
1.0
|
ND1
|
E:HIS150
|
3.8
|
32.2
|
1.0
|
CG
|
F:HIS150
|
4.1
|
31.3
|
1.0
|
ND1
|
F:HIS150
|
4.2
|
31.2
|
1.0
|
OG
|
E:SER145
|
4.2
|
39.1
|
1.0
|
CG
|
E:HIS150
|
4.2
|
32.6
|
1.0
|
OG
|
F:SER145
|
4.3
|
42.7
|
1.0
|
CB
|
E:ASP147
|
4.3
|
39.2
|
1.0
|
CB
|
F:ASP147
|
4.5
|
41.0
|
1.0
|
CB
|
E:SER145
|
4.6
|
39.0
|
1.0
|
CB
|
E:LYS149
|
4.9
|
41.3
|
1.0
|
CB
|
F:SER145
|
5.0
|
42.0
|
1.0
|
|
Zinc binding site 9 out
of 9 in 1u10
Go back to
Zinc Binding Sites List in 1u10
Zinc binding site 9 out
of 9 in the Mepa, Active Form with Zn in P1
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 9 of Mepa, Active Form with Zn in P1 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Zn400
b:18.9
occ:1.00
|
ND1
|
F:HIS110
|
2.0
|
24.5
|
1.0
|
NE2
|
F:HIS113
|
2.0
|
8.2
|
1.0
|
OD1
|
F:ASP120
|
2.0
|
5.7
|
1.0
|
ND1
|
F:HIS211
|
2.1
|
14.6
|
1.0
|
CG
|
F:ASP120
|
2.7
|
6.8
|
1.0
|
OD2
|
F:ASP120
|
2.8
|
8.3
|
1.0
|
CE1
|
F:HIS211
|
2.8
|
14.7
|
1.0
|
CE1
|
F:HIS110
|
2.8
|
27.7
|
1.0
|
CE1
|
F:HIS113
|
2.9
|
6.9
|
1.0
|
CD2
|
F:HIS113
|
3.1
|
8.2
|
1.0
|
CG
|
F:HIS110
|
3.1
|
25.8
|
1.0
|
CG
|
F:HIS211
|
3.3
|
14.5
|
1.0
|
CB
|
F:HIS110
|
3.6
|
24.8
|
1.0
|
CB
|
F:HIS211
|
3.8
|
12.7
|
1.0
|
NE2
|
F:HIS110
|
4.0
|
27.4
|
1.0
|
NE2
|
F:HIS211
|
4.0
|
15.4
|
1.0
|
ND1
|
F:HIS113
|
4.0
|
5.9
|
1.0
|
CB
|
F:ASP120
|
4.2
|
5.4
|
1.0
|
CD2
|
F:HIS110
|
4.2
|
26.3
|
1.0
|
CG
|
F:HIS113
|
4.2
|
7.4
|
1.0
|
CD2
|
F:HIS211
|
4.3
|
14.6
|
1.0
|
CA
|
F:HIS211
|
4.6
|
12.7
|
1.0
|
NE2
|
F:HIS206
|
4.6
|
24.4
|
1.0
|
CA
|
F:ASP120
|
4.7
|
9.0
|
1.0
|
N
|
F:ASP120
|
4.7
|
9.7
|
1.0
|
OG
|
F:SER112
|
5.0
|
14.2
|
1.0
|
|
Reference:
M.Marcyjaniak,
S.G.Odintsov,
I.Sabala,
M.Bochtler.
Peptidoglycan Amidase Mepa Is A Las Metallopeptidase J.Biol.Chem. V. 279 43982 2004.
ISSN: ISSN 0021-9258
PubMed: 15292190
DOI: 10.1074/JBC.M406735200
Page generated: Wed Oct 16 19:22:59 2024
|