Manganese in PDB 1nxd: Crystal Structure of Mnmn Concanavalin A
Protein crystallography data
The structure of Crystal Structure of Mnmn Concanavalin A, PDB code: 1nxd
was solved by
F.J.Lopez-Jaramillo,
L.A.Gonzalez-Ramirez,
A.Albert,
F.Santoyo-Gonzalez,
A.Vargas-Berenguel,
F.Otalora,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
19.00 /
1.90
|
Space group
|
C 2 2 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.300,
118.000,
249.500,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
18.4 /
20.1
|
Other elements in 1nxd:
The structure of Crystal Structure of Mnmn Concanavalin A also contains other interesting chemical elements:
Manganese Binding Sites:
The binding sites of Manganese atom in the Crystal Structure of Mnmn Concanavalin A
(pdb code 1nxd). This binding sites where shown within
5.0 Angstroms radius around Manganese atom.
In total 8 binding sites of Manganese where determined in the
Crystal Structure of Mnmn Concanavalin A, PDB code: 1nxd:
Jump to Manganese binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Manganese binding site 1 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 1 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 1 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mn1001
b:16.1
occ:1.00
|
OD1
|
1:ASN14
|
2.3
|
9.9
|
1.0
|
OD2
|
1:ASP19
|
2.4
|
9.4
|
1.0
|
O
|
1:TYR12
|
2.4
|
9.4
|
1.0
|
OD1
|
1:ASP10
|
2.4
|
8.0
|
1.0
|
O
|
1:HOH1063
|
2.5
|
9.2
|
1.0
|
OD2
|
1:ASP10
|
2.5
|
6.6
|
1.0
|
O
|
1:HOH1062
|
2.5
|
7.8
|
1.0
|
CG
|
1:ASP10
|
2.8
|
6.1
|
1.0
|
CG
|
1:ASN14
|
3.5
|
12.1
|
1.0
|
CG
|
1:ASP19
|
3.5
|
10.6
|
1.0
|
C
|
1:TYR12
|
3.5
|
9.9
|
1.0
|
N
|
1:ASN14
|
4.0
|
11.0
|
1.0
|
OD1
|
1:ASP19
|
4.0
|
8.9
|
1.0
|
CB
|
1:ASN14
|
4.1
|
11.9
|
1.0
|
MN
|
1:MN1002
|
4.2
|
10.1
|
1.0
|
CB
|
1:ASP10
|
4.3
|
6.3
|
1.0
|
CA
|
1:TYR12
|
4.3
|
9.9
|
1.0
|
N
|
1:TYR12
|
4.4
|
9.8
|
1.0
|
CB
|
1:TYR12
|
4.5
|
10.8
|
1.0
|
CB
|
1:ARG228
|
4.5
|
9.8
|
1.0
|
N
|
1:PRO13
|
4.6
|
9.8
|
1.0
|
ND2
|
1:ASN14
|
4.6
|
9.0
|
1.0
|
CE1
|
1:HIS24
|
4.6
|
9.2
|
1.0
|
O
|
1:ASP208
|
4.6
|
9.0
|
1.0
|
O
|
1:HOH1064
|
4.6
|
13.6
|
1.0
|
CA
|
1:ASN14
|
4.7
|
11.9
|
1.0
|
CB
|
1:ASP19
|
4.7
|
10.3
|
1.0
|
CA
|
1:PRO13
|
4.7
|
10.8
|
1.0
|
CA
|
1:ARG228
|
4.7
|
8.5
|
1.0
|
OD2
|
1:ASP208
|
4.7
|
8.8
|
1.0
|
C
|
1:PRO13
|
4.8
|
11.5
|
1.0
|
O
|
1:ARG228
|
4.8
|
8.4
|
1.0
|
NE2
|
1:HIS24
|
4.9
|
7.9
|
1.0
|
CD1
|
1:TYR12
|
5.0
|
12.7
|
1.0
|
|
Manganese binding site 2 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 2 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 2 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
1:Mn1002
b:10.1
occ:1.00
|
OD2
|
1:ASP10
|
2.1
|
6.6
|
1.0
|
OE2
|
1:GLU8
|
2.1
|
9.7
|
1.0
|
O
|
1:HOH1116
|
2.2
|
9.4
|
1.0
|
OD1
|
1:ASP19
|
2.3
|
8.9
|
1.0
|
NE2
|
1:HIS24
|
2.3
|
7.9
|
1.0
|
O
|
1:HOH1064
|
2.5
|
13.6
|
1.0
|
CG
|
1:ASP10
|
3.2
|
6.1
|
1.0
|
CD
|
1:GLU8
|
3.2
|
10.2
|
1.0
|
CG
|
1:ASP19
|
3.2
|
10.6
|
1.0
|
CE1
|
1:HIS24
|
3.3
|
9.2
|
1.0
|
CD2
|
1:HIS24
|
3.3
|
8.7
|
1.0
|
OE1
|
1:GLU8
|
3.5
|
9.4
|
1.0
|
CB
|
1:ASP10
|
3.5
|
6.3
|
1.0
|
OD2
|
1:ASP19
|
3.5
|
9.4
|
1.0
|
O
|
1:HOH1062
|
4.0
|
7.8
|
1.0
|
O
|
1:HOH1083
|
4.1
|
21.7
|
1.0
|
OG
|
1:SER34
|
4.2
|
10.6
|
1.0
|
MN
|
1:MN1001
|
4.2
|
16.1
|
1.0
|
O
|
1:HOH1077
|
4.3
|
23.0
|
1.0
|
OD1
|
1:ASP10
|
4.3
|
8.0
|
1.0
|
CB
|
1:ASP19
|
4.4
|
10.3
|
1.0
|
ND1
|
1:HIS24
|
4.4
|
8.3
|
1.0
|
CG
|
1:HIS24
|
4.5
|
8.4
|
1.0
|
CG
|
1:GLU8
|
4.5
|
8.5
|
1.0
|
O
|
1:VAL32
|
4.5
|
11.4
|
1.0
|
CA
|
1:ASP19
|
4.7
|
11.3
|
1.0
|
|
Manganese binding site 3 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 3 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 3 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mn1003
b:18.7
occ:1.00
|
OD2
|
2:ASP19
|
2.3
|
12.9
|
1.0
|
OD1
|
2:ASN14
|
2.4
|
12.4
|
1.0
|
O
|
2:TYR12
|
2.4
|
13.4
|
1.0
|
OD1
|
2:ASP10
|
2.4
|
10.8
|
1.0
|
O
|
2:HOH1046
|
2.4
|
11.5
|
1.0
|
O
|
2:HOH1014
|
2.5
|
12.9
|
1.0
|
OD2
|
2:ASP10
|
2.6
|
8.3
|
1.0
|
CG
|
2:ASP10
|
2.8
|
10.9
|
1.0
|
CG
|
2:ASP19
|
3.5
|
13.0
|
1.0
|
CG
|
2:ASN14
|
3.5
|
14.0
|
1.0
|
C
|
2:TYR12
|
3.6
|
14.5
|
1.0
|
N
|
2:ASN14
|
3.9
|
14.7
|
1.0
|
OD1
|
2:ASP19
|
4.0
|
12.1
|
1.0
|
CB
|
2:ASN14
|
4.0
|
14.0
|
1.0
|
MN
|
2:MN1004
|
4.2
|
12.4
|
1.0
|
CB
|
2:ASP10
|
4.3
|
11.3
|
1.0
|
CA
|
2:TYR12
|
4.5
|
13.8
|
1.0
|
N
|
2:PRO13
|
4.5
|
14.4
|
1.0
|
N
|
2:TYR12
|
4.5
|
13.3
|
1.0
|
CA
|
2:PRO13
|
4.6
|
14.6
|
1.0
|
C
|
2:PRO13
|
4.6
|
15.9
|
1.0
|
ND2
|
2:ASN14
|
4.6
|
12.3
|
1.0
|
CA
|
2:ASN14
|
4.6
|
14.9
|
1.0
|
CB
|
2:ASP19
|
4.7
|
13.1
|
1.0
|
CB
|
2:ARG228
|
4.7
|
13.9
|
1.0
|
CE1
|
2:HIS24
|
4.7
|
11.3
|
1.0
|
OD2
|
2:ASP208
|
4.7
|
13.3
|
1.0
|
CB
|
2:TYR12
|
4.7
|
14.1
|
1.0
|
O
|
2:ASP208
|
4.7
|
13.1
|
1.0
|
O
|
2:HOH1035
|
4.8
|
14.7
|
1.0
|
O
|
2:ARG228
|
4.8
|
16.4
|
1.0
|
CA
|
2:ARG228
|
4.9
|
14.7
|
1.0
|
CD1
|
2:TYR12
|
4.9
|
14.1
|
1.0
|
|
Manganese binding site 4 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 4 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 4 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
2:Mn1004
b:12.4
occ:1.00
|
OD2
|
2:ASP10
|
2.1
|
8.3
|
1.0
|
O
|
2:HOH1092
|
2.1
|
12.3
|
1.0
|
OE2
|
2:GLU8
|
2.2
|
10.9
|
1.0
|
OD1
|
2:ASP19
|
2.3
|
12.1
|
1.0
|
NE2
|
2:HIS24
|
2.3
|
12.0
|
1.0
|
O
|
2:HOH1035
|
2.4
|
14.7
|
1.0
|
CG
|
2:ASP19
|
3.1
|
13.0
|
1.0
|
CG
|
2:ASP10
|
3.1
|
10.9
|
1.0
|
CE1
|
2:HIS24
|
3.1
|
11.3
|
1.0
|
CD
|
2:GLU8
|
3.2
|
12.3
|
1.0
|
CD2
|
2:HIS24
|
3.4
|
11.3
|
1.0
|
OD2
|
2:ASP19
|
3.5
|
12.9
|
1.0
|
CB
|
2:ASP10
|
3.5
|
11.3
|
1.0
|
OE1
|
2:GLU8
|
3.6
|
12.2
|
1.0
|
O
|
2:HOH1046
|
3.9
|
11.5
|
1.0
|
O
|
2:HOH1058
|
4.0
|
24.0
|
1.0
|
MN
|
2:MN1003
|
4.2
|
18.7
|
1.0
|
OG
|
2:SER34
|
4.2
|
12.5
|
1.0
|
OD1
|
2:ASP10
|
4.2
|
10.8
|
1.0
|
ND1
|
2:HIS24
|
4.3
|
12.1
|
1.0
|
O
|
2:HOH1184
|
4.3
|
36.1
|
1.0
|
CB
|
2:ASP19
|
4.3
|
13.1
|
1.0
|
CG
|
2:HIS24
|
4.5
|
13.0
|
1.0
|
CG
|
2:GLU8
|
4.6
|
9.9
|
1.0
|
O
|
2:VAL32
|
4.7
|
14.0
|
1.0
|
CA
|
2:ASP19
|
4.7
|
14.3
|
1.0
|
|
Manganese binding site 5 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 5 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 5 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Mn1005
b:24.8
occ:1.00
|
OD1
|
3:ASN14
|
2.3
|
16.8
|
1.0
|
O
|
3:TYR12
|
2.4
|
15.3
|
1.0
|
O
|
3:HOH1028
|
2.4
|
14.0
|
1.0
|
OD1
|
3:ASP10
|
2.4
|
10.8
|
1.0
|
OD2
|
3:ASP19
|
2.6
|
16.9
|
1.0
|
O
|
3:HOH1030
|
2.6
|
17.4
|
1.0
|
OD2
|
3:ASP10
|
2.7
|
11.8
|
1.0
|
CG
|
3:ASP10
|
2.9
|
10.6
|
1.0
|
CG
|
3:ASN14
|
3.4
|
18.8
|
1.0
|
C
|
3:TYR12
|
3.5
|
15.0
|
1.0
|
CG
|
3:ASP19
|
3.7
|
17.2
|
1.0
|
N
|
3:ASN14
|
4.0
|
17.6
|
1.0
|
CB
|
3:ASN14
|
4.1
|
18.8
|
1.0
|
CA
|
3:TYR12
|
4.3
|
15.0
|
1.0
|
OD1
|
3:ASP19
|
4.3
|
15.3
|
1.0
|
N
|
3:TYR12
|
4.3
|
13.4
|
1.0
|
CB
|
3:ASP10
|
4.4
|
11.3
|
1.0
|
MN
|
3:MN1006
|
4.4
|
16.0
|
1.0
|
CB
|
3:TYR12
|
4.4
|
16.4
|
1.0
|
O
|
3:ASP208
|
4.5
|
11.5
|
1.0
|
ND2
|
3:ASN14
|
4.5
|
18.4
|
1.0
|
N
|
3:PRO13
|
4.6
|
15.4
|
1.0
|
OD2
|
3:ASP208
|
4.6
|
16.6
|
1.0
|
CB
|
3:ARG228
|
4.7
|
20.3
|
1.0
|
CA
|
3:ASN14
|
4.7
|
18.7
|
1.0
|
CA
|
3:ARG228
|
4.7
|
18.2
|
1.0
|
O
|
3:ARG228
|
4.7
|
17.9
|
1.0
|
CA
|
3:PRO13
|
4.7
|
15.4
|
1.0
|
C
|
3:PRO13
|
4.8
|
17.7
|
1.0
|
CE1
|
3:HIS24
|
4.8
|
14.3
|
1.0
|
CD1
|
3:TYR12
|
4.8
|
18.8
|
1.0
|
O
|
3:HOH1029
|
4.8
|
17.4
|
1.0
|
CB
|
3:ASP19
|
4.9
|
17.4
|
1.0
|
|
Manganese binding site 6 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 6 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 6 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
3:Mn1006
b:16.0
occ:1.00
|
OD2
|
3:ASP10
|
2.1
|
11.8
|
1.0
|
OE2
|
3:GLU8
|
2.2
|
15.4
|
1.0
|
O
|
3:HOH1069
|
2.2
|
15.4
|
1.0
|
O
|
3:HOH1029
|
2.2
|
17.4
|
1.0
|
OD1
|
3:ASP19
|
2.3
|
15.3
|
1.0
|
NE2
|
3:HIS24
|
2.3
|
14.1
|
1.0
|
CG
|
3:ASP19
|
3.1
|
17.2
|
1.0
|
CG
|
3:ASP10
|
3.2
|
10.6
|
1.0
|
CE1
|
3:HIS24
|
3.2
|
14.3
|
1.0
|
CD
|
3:GLU8
|
3.2
|
15.1
|
1.0
|
CD2
|
3:HIS24
|
3.4
|
12.7
|
1.0
|
OD2
|
3:ASP19
|
3.4
|
16.9
|
1.0
|
OE1
|
3:GLU8
|
3.6
|
15.2
|
1.0
|
CB
|
3:ASP10
|
3.6
|
11.3
|
1.0
|
O
|
3:HOH1030
|
4.0
|
17.4
|
1.0
|
OG
|
3:SER34
|
4.2
|
16.7
|
1.0
|
OD1
|
3:ASP10
|
4.3
|
10.8
|
1.0
|
CB
|
3:ASP19
|
4.3
|
17.4
|
1.0
|
ND1
|
3:HIS24
|
4.4
|
11.4
|
1.0
|
O
|
3:HOH1170
|
4.4
|
42.3
|
1.0
|
MN
|
3:MN1005
|
4.4
|
24.8
|
1.0
|
CG
|
3:HIS24
|
4.5
|
12.6
|
1.0
|
O
|
3:VAL32
|
4.5
|
17.9
|
1.0
|
CG
|
3:GLU8
|
4.5
|
12.9
|
1.0
|
CA
|
3:ASP19
|
4.7
|
17.8
|
1.0
|
|
Manganese binding site 7 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 7 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 7 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Mn1007
b:18.8
occ:1.00
|
O
|
4:HOH1045
|
2.2
|
8.9
|
1.0
|
OD1
|
4:ASN14
|
2.3
|
11.3
|
1.0
|
O
|
4:TYR12
|
2.3
|
10.8
|
1.0
|
OD2
|
4:ASP19
|
2.4
|
14.2
|
1.0
|
OD1
|
4:ASP10
|
2.5
|
8.5
|
1.0
|
O
|
4:HOH1012
|
2.5
|
10.0
|
1.0
|
OD2
|
4:ASP10
|
2.6
|
7.7
|
1.0
|
CG
|
4:ASP10
|
2.9
|
8.4
|
1.0
|
CG
|
4:ASN14
|
3.4
|
12.5
|
1.0
|
C
|
4:TYR12
|
3.5
|
12.1
|
1.0
|
CG
|
4:ASP19
|
3.6
|
12.2
|
1.0
|
N
|
4:ASN14
|
4.0
|
14.2
|
1.0
|
CB
|
4:ASN14
|
4.1
|
13.6
|
1.0
|
OD1
|
4:ASP19
|
4.1
|
11.3
|
1.0
|
CA
|
4:TYR12
|
4.3
|
12.1
|
1.0
|
MN
|
4:MN1008
|
4.3
|
11.9
|
1.0
|
CB
|
4:ASP10
|
4.4
|
10.0
|
1.0
|
N
|
4:TYR12
|
4.4
|
11.4
|
1.0
|
N
|
4:PRO13
|
4.5
|
12.9
|
1.0
|
CB
|
4:TYR12
|
4.5
|
12.2
|
1.0
|
ND2
|
4:ASN14
|
4.5
|
11.6
|
1.0
|
OD2
|
4:ASP208
|
4.5
|
10.3
|
1.0
|
CA
|
4:PRO13
|
4.6
|
14.1
|
1.0
|
O
|
4:ASP208
|
4.6
|
9.2
|
1.0
|
C
|
4:PRO13
|
4.6
|
14.6
|
1.0
|
CB
|
4:ARG228
|
4.6
|
10.8
|
1.0
|
CA
|
4:ASN14
|
4.7
|
14.0
|
1.0
|
CB
|
4:ASP19
|
4.8
|
13.0
|
1.0
|
O
|
4:ARG228
|
4.8
|
12.3
|
1.0
|
CD1
|
4:TYR12
|
4.8
|
14.0
|
1.0
|
CE1
|
4:HIS24
|
4.8
|
11.1
|
1.0
|
CA
|
4:ARG228
|
4.8
|
11.6
|
1.0
|
O
|
4:HOH1044
|
4.8
|
8.1
|
1.0
|
O3
|
4:GOL805
|
4.9
|
21.1
|
1.0
|
|
Manganese binding site 8 out
of 8 in 1nxd
Go back to
Manganese Binding Sites List in 1nxd
Manganese binding site 8 out
of 8 in the Crystal Structure of Mnmn Concanavalin A
Mono view
Stereo pair view
|
A full contact list of Manganese with other atoms in the Mn binding
site number 8 of Crystal Structure of Mnmn Concanavalin A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
4:Mn1008
b:11.9
occ:1.00
|
O
|
4:HOH1108
|
2.0
|
9.7
|
1.0
|
OD2
|
4:ASP10
|
2.2
|
7.7
|
1.0
|
OE2
|
4:GLU8
|
2.2
|
9.6
|
1.0
|
OD1
|
4:ASP19
|
2.2
|
11.3
|
1.0
|
NE2
|
4:HIS24
|
2.3
|
12.9
|
1.0
|
O
|
4:HOH1044
|
2.4
|
8.1
|
1.0
|
CG
|
4:ASP19
|
3.1
|
12.2
|
1.0
|
CD
|
4:GLU8
|
3.2
|
12.4
|
1.0
|
CG
|
4:ASP10
|
3.2
|
8.4
|
1.0
|
CE1
|
4:HIS24
|
3.2
|
11.1
|
1.0
|
CD2
|
4:HIS24
|
3.3
|
10.6
|
1.0
|
OD2
|
4:ASP19
|
3.4
|
14.2
|
1.0
|
OE1
|
4:GLU8
|
3.5
|
11.6
|
1.0
|
CB
|
4:ASP10
|
3.6
|
10.0
|
1.0
|
O
|
4:HOH1012
|
4.0
|
10.0
|
1.0
|
O
|
4:HOH1174
|
4.2
|
24.9
|
1.0
|
OG
|
4:SER34
|
4.2
|
10.0
|
1.0
|
OD1
|
4:ASP10
|
4.3
|
8.5
|
1.0
|
MN
|
4:MN1007
|
4.3
|
18.8
|
1.0
|
ND1
|
4:HIS24
|
4.3
|
10.0
|
1.0
|
CB
|
4:ASP19
|
4.4
|
13.0
|
1.0
|
CG
|
4:HIS24
|
4.4
|
13.2
|
1.0
|
CG
|
4:GLU8
|
4.5
|
8.9
|
1.0
|
O
|
4:VAL32
|
4.6
|
12.0
|
1.0
|
O
|
4:HOH1133
|
4.7
|
35.1
|
1.0
|
CA
|
4:ASP19
|
4.7
|
14.6
|
1.0
|
CD
|
4:PRO20
|
5.0
|
18.9
|
1.0
|
|
Reference:
F.J.Lopez-Jaramillo,
L.A.Gonzalez-Ramirez,
A.Albert,
F.Santoyo-Gonzalez,
A.Vargas-Berenguel,
F.Otalora.
Structure of Concanavalin A at pH 8: Bound Solvent and Crystal Contacts. Acta Crystallogr.,Sect.D V. 60 1048 2004.
ISSN: ISSN 0907-4449
PubMed: 15159564
DOI: 10.1107/S0907444904007000
Page generated: Sat Oct 5 11:53:15 2024
|