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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:

Sodium (Na) 4 atoms

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

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Manganese binding site 1 out of 8 in the Crystal Structure of Mnmn Concanavalin A


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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

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Manganese binding site 2 out of 8 in the Crystal Structure of Mnmn Concanavalin A


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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

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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

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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

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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

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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

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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

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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

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