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Sodium in PDB 3ud2: Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin

Protein crystallography data

The structure of Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin, PDB code: 3ud2 was solved by M.Yasunaga, J.J.Ipsaro, A.Mondragon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.90 / 2.21
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 279.480, 40.873, 95.249, 90.00, 92.01, 90.00
R / Rfree (%) 22.1 / 25.9

Other elements in 3ud2:

The structure of Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin (pdb code 3ud2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 17 binding sites of Sodium where determined in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin, PDB code: 3ud2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 17 in 3ud2

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Sodium binding site 1 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na8

b:43.1
occ:1.00
 O C:ARG1004 3.0 22.2 1.0
O C:GLY1002 3.5 25.4 1.0
SG C:CYS1070 3.7 33.4 1.0
C C:ARG1001 3.7 30.6 1.0
C C:ARG1004 3.8 22.9 1.0
O C:ARG1001 3.8 32.7 1.0
CA C:ARG1001 3.8 31.6 1.0
CB C:ARG1001 3.9 34.7 1.0
CB C:GLU1005 4.0 22.1 1.0
CA C:GLU1005 4.0 21.3 1.0
N C:GLY1002 4.0 29.0 1.0
N C:GLU1005 4.2 22.7 1.0
C C:GLY1002 4.3 27.4 1.0
O C:HOH148 4.3 20.6 1.0
CG C:ARG1001 4.4 39.3 1.0
O C:HOH72 4.5 24.6 1.0
NE2 C:GLN1109 4.5 36.3 1.0
N C:ARG1004 4.6 24.9 1.0
CA C:GLY1002 4.6 28.3 1.0
CA C:ARG1004 4.8 24.2 1.0

Sodium binding site 2 out of 17 in 3ud2

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Sodium binding site 2 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na1

b:21.6
occ:1.00
 O B:ILE1177 2.6 22.2 1.0
OG B:SER1175 2.8 21.4 1.0
O B:GLN1182 3.0 22.9 1.0
NE B:ARG1210 3.4 17.8 1.0
C B:ILE1177 3.6 23.7 1.0
CB B:SER1175 3.6 21.9 1.0
CG1 B:ILE1177 3.7 24.1 1.0
O B:SER1175 3.7 21.6 1.0
N B:ILE1177 3.7 23.9 1.0
NH2 B:ARG1137 3.7 23.9 1.0
CA B:ALA1183 3.8 23.4 1.0
NE B:ARG1137 3.8 23.6 1.0
CG B:ARG1210 3.8 18.1 1.0
CD B:ARG1210 3.9 17.8 1.0
C B:GLN1182 3.9 23.9 1.0
C B:SER1175 3.9 22.3 1.0
CA B:ILE1177 4.0 24.3 1.0
CZ B:ARG1210 4.1 17.6 1.0
CZ B:ARG1137 4.2 23.0 1.0
CB B:ALA1183 4.2 22.1 1.0
C B:VAL1176 4.2 24.1 1.0
N B:ALA1183 4.3 23.8 1.0
NH2 B:ARG1210 4.3 18.0 1.0
N B:VAL1176 4.4 23.4 1.0
CA B:SER1175 4.5 22.2 1.0
CB B:ILE1177 4.5 24.9 1.0
CB B:ARG1210 4.7 18.1 1.0
N B:GLN1184 4.7 25.3 1.0
C B:ALA1183 4.8 24.4 1.0
N B:GLY1178 4.8 24.2 1.0
CA B:VAL1176 4.8 23.9 1.0
O B:VAL1176 4.8 24.4 1.0
CD B:ARG1137 4.8 23.4 1.0
CD1 B:ILE1177 4.8 24.4 1.0

Sodium binding site 3 out of 17 in 3ud2

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Sodium binding site 3 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na2

b:24.9
occ:1.00
 OG1 B:THR1133 2.7 17.1 1.0
NA B:NA11 2.7 30.1 1.0
O B:ILE1131 3.1 16.7 1.0
O B:GLN1109 3.5 23.4 1.0
NE2 B:GLN1109 3.5 24.6 1.0
CB B:THR1133 3.6 17.0 1.0
CG2 B:ILE1131 3.7 17.9 1.0
N B:THR1133 3.7 16.3 1.0
C B:ILE1131 3.7 16.9 1.0
CB B:ILE1131 4.0 17.5 1.0
CG B:GLN1109 4.1 23.8 1.0
C B:GLN1109 4.1 22.2 1.0
N B:GLN1111 4.1 22.2 1.0
C B:VAL1132 4.2 16.4 1.0
CD B:GLN1109 4.2 25.6 1.0
N B:VAL1132 4.3 16.6 1.0
NH1 B:ARG1210 4.3 17.2 1.0
CA B:THR1133 4.3 16.8 1.0
CB B:GLN1109 4.3 22.9 1.0
CA B:VAL1132 4.3 16.0 1.0
CB B:GLN1111 4.3 24.7 1.0
CA B:ILE1131 4.6 17.5 1.0
CA B:ALA1110 4.6 20.9 1.0
N B:ALA1110 4.6 20.9 1.0
C B:ALA1110 4.7 21.6 1.0
CA B:GLN1111 4.9 23.0 1.0
NA B:NA9 4.9 28.7 1.0
CG2 B:THR1133 4.9 17.3 1.0
CA B:GLN1109 4.9 22.1 1.0
OD1 B:ASP1003 4.9 20.9 1.0
OE1 B:GLN1111 5.0 26.7 1.0

Sodium binding site 4 out of 17 in 3ud2

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Sodium binding site 4 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na3

b:24.9
occ:1.00
 OD2 B:ASP1181 2.4 26.1 1.0
O B:GLY1000 3.0 24.5 1.0
N B:ARG1004 3.2 20.8 1.0
CG B:ASP1181 3.2 25.0 1.0
OD1 B:ASP1181 3.3 24.5 1.0
N B:GLY1002 3.3 23.9 1.0
N B:ASP1003 3.4 21.0 1.0
C B:GLY1000 3.7 25.0 1.0
CB B:ARG1004 3.7 22.6 1.0
O B:ARG1004 3.7 21.0 1.0
CA B:GLY1002 3.8 23.3 1.0
ND1 B:HIS999 3.8 19.0 1.0
C B:GLY1002 3.8 21.4 1.0
NE B:ARG1004 3.8 26.3 1.0
CA B:ARG1004 3.9 21.5 1.0
CB B:HIS999 3.9 22.2 1.0
CG B:HIS999 4.0 20.5 1.0
N B:GLY1000 4.2 23.0 1.0
C B:ASP1003 4.2 21.1 1.0
C B:ARG1004 4.2 20.5 1.0
NH2 B:ARG1004 4.2 28.3 1.0
CA B:ASP1003 4.3 21.1 1.0
N B:ARG1001 4.4 25.8 1.0
C B:ARG1001 4.4 25.6 1.0
CG B:ARG1004 4.4 24.3 1.0
CA B:GLY1000 4.5 24.0 1.0
CZ B:ARG1004 4.5 28.0 1.0
CA B:ARG1001 4.6 27.7 1.0
O B:GLY1002 4.6 20.1 1.0
CD B:ARG1004 4.7 25.4 1.0
CE1 B:HIS999 4.7 19.1 1.0
CB B:ASP1181 4.7 24.9 1.0
NA B:NA13 4.7 31.7 1.0
CB B:ASP1003 4.7 21.8 1.0
C B:HIS999 4.8 23.5 1.0
CA B:HIS999 5.0 23.4 1.0

Sodium binding site 5 out of 17 in 3ud2

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Sodium binding site 5 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na4

b:39.8
occ:1.00
 O B:ALA1197 2.9 32.4 1.0
ND2 B:ASN1202 3.1 28.1 1.0
OD1 B:ASN1202 3.4 28.1 1.0
CD B:ARG1148 3.6 30.3 1.0
CG B:ASN1202 3.6 27.3 1.0
C B:ALA1197 3.6 33.3 1.0
CB B:ALA1197 3.7 34.2 1.0
CA B:ALA1197 4.1 33.5 1.0
CG B:ARG1148 4.2 28.1 1.0
CB B:CYS1200 4.3 26.5 1.0
N B:ALA1197 4.3 32.6 1.0
CB B:ASN1198 4.3 34.2 1.0
N B:ASN1198 4.5 33.4 1.0
OD1 B:ASN1198 4.5 35.1 1.0
NH1 B:ARG1148 4.7 36.1 1.0
O B:CYS1200 4.8 27.0 1.0
NE B:ARG1148 4.8 32.0 1.0
CA B:ASN1198 4.9 33.6 1.0
CG B:ASN1198 4.9 34.9 1.0

Sodium binding site 6 out of 17 in 3ud2

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Sodium binding site 6 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na5

b:30.4
occ:1.00
 NA B:NA16 2.7 31.4 1.0
O B:GLY1000 3.0 24.5 1.0
O B:ARG1004 3.4 21.0 1.0
CE1 B:HIS999 3.6 19.1 1.0
CG B:ARG1001 3.7 35.5 1.0
C B:GLY1000 3.7 25.0 1.0
CA B:GLU1005 3.7 18.6 1.0
ND1 B:HIS999 3.7 19.0 1.0
CA B:ARG1001 3.8 27.7 1.0
N B:LEU1006 3.9 16.7 1.0
N B:ARG1001 4.0 25.8 1.0
C B:GLU1005 4.1 17.6 1.0
C B:ARG1004 4.1 20.5 1.0
CG B:LEU1006 4.1 16.2 1.0
N B:GLU1005 4.2 19.7 1.0
CB B:ARG1001 4.3 30.5 1.0
NA B:NA10 4.3 35.5 1.0
CB B:LEU1006 4.7 16.0 1.0
CD2 B:LEU1006 4.7 16.1 1.0
O B:HIS999 4.8 21.5 1.0
CD1 B:LEU1006 4.8 15.8 1.0
CA B:GLY1000 4.8 24.0 1.0
CB B:GLU1005 4.9 18.9 1.0
O B:GLU1005 4.9 16.9 1.0
NE2 B:HIS999 4.9 19.4 1.0
CA B:LEU1006 4.9 16.5 1.0
C B:ARG1001 5.0 25.6 1.0

Sodium binding site 7 out of 17 in 3ud2

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Sodium binding site 7 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na6

b:36.5
occ:1.00
 O B:ALA1220 2.5 36.1 1.0
N B:ASN1224 3.3 30.8 1.0
C B:GLU1221 3.4 33.8 1.0
CA B:GLU1221 3.4 36.2 1.0
CG B:ASN1224 3.5 35.6 1.0
ND2 B:ASN1224 3.5 37.0 1.0
C B:ALA1220 3.5 36.7 1.0
O B:GLU1221 3.6 32.8 1.0
N B:VAL1223 3.6 29.8 1.0
CB B:VAL1223 3.7 30.5 1.0
OD1 B:ASN1224 3.8 35.8 1.0
N B:ALA1222 3.9 32.2 1.0
CB B:ASN1224 3.9 33.9 1.0
N B:GLU1221 3.9 36.7 1.0
CA B:VAL1223 4.0 29.4 1.0
C B:VAL1223 4.0 29.8 1.0
CA B:ASN1224 4.2 31.3 1.0
C B:ALA1222 4.5 29.5 1.0
CG1 B:VAL1223 4.5 30.3 1.0
CB B:GLU1221 4.7 37.4 1.0
CA B:ALA1222 4.8 30.6 1.0
CG2 B:VAL1223 4.8 29.6 1.0
CD B:GLU1221 4.8 40.8 1.0
OE2 B:GLU1221 4.8 43.4 1.0
CA B:ALA1220 4.9 37.3 1.0
OE1 B:GLU1221 4.9 40.5 1.0

Sodium binding site 8 out of 17 in 3ud2

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Sodium binding site 8 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


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 Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na9

b:28.7
occ:1.00
 OH B:TYR1230 2.7 19.9 1.0
NA B:NA11 2.7 30.1 1.0
NA B:NA13 2.8 31.7 1.0
OD1 B:ASP1181 2.9 24.5 1.0
OD1 B:ASP1003 3.3 20.9 1.0
NH1 B:ARG1210 3.4 17.2 1.0
CZ B:ARG1210 3.4 17.6 1.0
NH2 B:ARG1210 3.5 18.0 1.0
CZ B:TYR1230 3.6 20.1 1.0
CE2 B:TYR1230 3.6 19.9 1.0
CG B:ASP1003 3.8 22.1 1.0
CG B:ASP1181 3.9 25.0 1.0
CA B:ASP1181 3.9 24.4 1.0
OD2 B:ASP1003 4.0 22.2 1.0
NE B:ARG1210 4.1 17.8 1.0
N B:ASP1003 4.2 21.0 1.0
OE1 B:GLN1111 4.2 26.7 1.0
CA B:GLY1002 4.2 23.3 1.0
CB B:ASP1181 4.3 24.9 1.0
C B:GLY1002 4.6 21.4 1.0
N B:ASP1181 4.6 23.3 1.0
CD B:ARG1210 4.7 17.8 1.0
NE2 B:GLN1109 4.7 24.6 1.0
C B:ASP1181 4.7 24.8 1.0
CE1 B:TYR1230 4.8 20.8 1.0
CB B:ASP1003 4.8 21.8 1.0
NA B:NA2 4.9 24.9 1.0
CD2 B:TYR1230 4.9 20.2 1.0
OD2 B:ASP1181 5.0 26.1 1.0

Sodium binding site 9 out of 17 in 3ud2

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Sodium binding site 9 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na10

b:35.5
occ:1.00
 O B:ARG1004 3.0 21.0 1.0
O B:GLY1002 3.5 20.1 1.0
C B:ARG1001 3.6 25.6 1.0
CA B:ARG1001 3.7 27.7 1.0
SG B:CYS1070 3.7 26.9 1.0
CB B:GLU1005 3.8 18.9 1.0
O B:ARG1001 3.8 24.5 1.0
C B:ARG1004 3.8 20.5 1.0
CA B:GLU1005 3.9 18.6 1.0
CB B:ARG1001 3.9 30.5 1.0
N B:GLY1002 4.0 23.9 1.0
N B:GLU1005 4.2 19.7 1.0
NA B:NA5 4.3 30.4 1.0
C B:GLY1002 4.3 21.4 1.0
CG B:ARG1001 4.4 35.5 1.0
CD1 B:LEU1087 4.5 45.0 1.0
CA B:GLY1002 4.6 23.3 1.0
N B:ARG1004 4.9 20.8 1.0
CA B:ARG1004 5.0 21.5 1.0

Sodium binding site 10 out of 17 in 3ud2

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Sodium binding site 10 out of 17 in the Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Crystal Structure of Selenomethionine ZU5A-ZU5B Protein Domains of Human Erythrocyte Ankyrin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na11

b:30.1
occ:1.00
 NA B:NA2 2.7 24.9 1.0
NA B:NA9 2.7 28.7 1.0
OE1 B:GLN1111 2.8 26.7 1.0
CB B:GLN1111 3.8 24.7 1.0
NA B:NA13 3.8 31.7 1.0
CG2 B:ILE1131 3.8 17.9 1.0
CD B:GLN1111 3.9 25.8 1.0
CA B:GLY1002 3.9 23.3 1.0
CB B:ILE1131 4.0 17.5 1.0
NH1 B:ARG1210 4.1 17.2 1.0
NE2 B:GLN1109 4.1 24.6 1.0
CD1 B:ILE1131 4.2 18.1 1.0
OG1 B:THR1133 4.4 17.1 1.0
CG B:GLN1111 4.4 24.9 1.0
OD1 B:ASP1003 4.5 20.9 1.0
CE2 B:TYR1230 4.5 19.9 1.0
C B:GLY1002 4.7 21.4 1.0
CG1 B:ILE1131 4.7 18.1 1.0
O B:ILE1131 4.8 16.7 1.0
CZ B:ARG1210 4.8 17.6 1.0
OH B:TYR1230 4.8 19.9 1.0
CD B:ARG1210 4.9 17.8 1.0
N B:ASP1003 5.0 21.0 1.0

Reference:

M.Yasunaga, J.J.Ipsaro, A.Mondragon. Structurally Similar But Functionally Diverse ZU5 Domains in Human Erythrocyte Ankyrin. J.Mol.Biol. V. 417 336 2012.
ISSN: ISSN 0022-2836
PubMed: 22310050
DOI: 10.1016/J.JMB.2012.01.041
Page generated: Mon Oct 7 13:27:06 2024

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