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Sodium in PDB 1gq2: Malic Enzyme From Pigeon Liver

Enzymatic activity of Malic Enzyme From Pigeon Liver

All present enzymatic activity of Malic Enzyme From Pigeon Liver:
1.1.1.40;

Protein crystallography data

The structure of Malic Enzyme From Pigeon Liver, PDB code: 1gq2 was solved by Z.Yang, H.Zhang, T.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10 / 2.5
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 124.149, 140.863, 167.079, 90.05, 87.16, 75.63
R / Rfree (%) 21 / 25.6

Other elements in 1gq2:

The structure of Malic Enzyme From Pigeon Liver also contains other interesting chemical elements:

Manganese (Mn) 16 atoms
Chlorine (Cl) 33 atoms

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 36;

Binding sites:

The binding sites of Sodium atom in the Malic Enzyme From Pigeon Liver (pdb code 1gq2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 36 binding sites of Sodium where determined in the Malic Enzyme From Pigeon Liver, PDB code: 1gq2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 1 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1584

b:16.7
occ:1.00
 O C:PHE72 2.8 18.8 1.0
NE C:ARG81 2.8 16.8 1.0
O C:HOH2014 3.1 3.8 1.0
O C:LEU75 3.2 13.2 1.0
O C:GLU73 3.2 21.0 1.0
NH2 C:ARG81 3.4 17.2 1.0
CZ C:ARG81 3.6 18.1 1.0
C C:GLU73 3.7 19.7 1.0
C C:PHE72 3.8 19.4 1.0
CD C:ARG81 3.8 14.2 1.0
CA C:GLU73 3.9 20.9 1.0
CD2 C:PHE72 4.1 20.4 1.0
C C:LEU75 4.1 13.6 1.0
N C:GLU73 4.2 20.4 1.0
N C:LEU75 4.2 15.5 1.0
CE2 C:PHE72 4.2 20.0 1.0
CA C:LEU75 4.5 14.2 1.0
CB C:LEU75 4.6 14.8 1.0
CG C:ARG81 4.7 13.6 1.0
O C:HOH2016 4.8 1.7 1.0
N C:ARG74 4.8 17.1 1.0
NH1 C:ARG81 4.9 19.2 1.0
CG C:PHE72 4.9 18.9 1.0

Sodium binding site 2 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 2 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1585

b:14.7
occ:1.00
 O C:ILE350 2.7 21.1 1.0
O C:PHE365 2.8 22.6 1.0
N C:MSE343 3.0 18.6 1.0
CA C:TRP342 3.5 17.7 1.0
O C:MSE343 3.6 17.6 1.0
C C:ILE350 3.7 21.6 1.0
C C:TRP342 3.8 18.3 1.0
CB C:ILE350 3.8 19.1 1.0
CE3 C:TRP342 3.8 20.9 1.0
C C:PHE365 3.9 22.5 1.0
CB C:TRP342 4.0 19.1 1.0
CA C:MSE343 4.0 17.6 1.0
CD2 C:HIS367 4.0 23.3 1.0
CA C:ILE350 4.1 20.2 1.0
CG2 C:ILE350 4.2 15.7 1.0
N C:ILE350 4.2 19.8 1.0
C C:MSE343 4.3 17.6 1.0
CB C:PHE365 4.3 18.6 1.0
CB C:MSE343 4.4 18.9 1.0
O C:ILE341 4.4 17.3 1.0
CD2 C:TRP342 4.4 21.0 1.0
NE2 C:HIS367 4.5 24.5 1.0
CG C:TRP342 4.6 20.5 1.0
CD1 C:LEU349 4.6 10.8 1.0
N C:HIS367 4.6 27.0 1.0
CA C:ALA366 4.7 25.1 1.0
CZ3 C:TRP342 4.7 22.9 1.0
N C:ALA366 4.7 23.6 1.0
N C:TRP342 4.7 17.6 1.0
CG C:HIS367 4.7 25.3 1.0
CA C:PHE365 4.8 22.1 1.0
CG C:MSE343 4.8 21.4 1.0
N C:VAL351 4.9 22.4 1.0
O C:TRP342 5.0 19.0 1.0
CG C:LEU349 5.0 16.7 1.0
C C:ILE341 5.0 17.5 1.0

Sodium binding site 3 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 3 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1586

b:15.7
occ:1.00
 O C:ASN271 2.8 17.8 1.0
CD2 C:HIS485 3.5 10.5 1.0
NE2 C:HIS485 3.6 8.5 1.0
C C:ASN271 3.8 18.2 1.0
CB C:ASN271 3.9 19.2 1.0
CA C:ASN271 4.2 17.8 1.0
CG C:HIS485 4.3 12.0 1.0
CE1 C:HIS485 4.3 9.7 1.0
ND1 C:HIS485 4.7 11.9 1.0
OD1 C:ASN271 4.8 22.3 1.0
CG C:ASN271 4.8 19.7 1.0

Sodium binding site 4 out of 36 in 1gq2

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Sodium binding site 4 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na1587

b:16.3
occ:1.00
 OH C:TYR123 2.8 3.5 1.0
OH C:TYR82 3.0 9.9 1.0
CE1 C:TYR123 3.4 2.5 1.0
CE C:MSE86 3.5 25.8 1.0
CZ C:TYR123 3.5 3.7 1.0
CG1 C:VAL181 3.8 13.2 1.0
CG2 C:VAL181 3.8 11.7 1.0
CB C:VAL181 3.9 11.6 1.0
SE C:MSE86 4.0 36.0 1.0
CZ C:TYR82 4.2 12.0 1.0
CA C:GLY178 4.3 11.4 1.0
CG C:MSE86 4.5 25.1 1.0
O C:HOH2008 4.6 4.0 1.0
CD1 C:TYR123 4.7 5.3 1.0
CE2 C:TYR82 4.7 13.5 1.0
O C:HOH2011 4.8 24.5 1.0
CE2 C:TYR123 4.8 3.5 1.0
N C:GLY178 4.9 11.3 1.0

Sodium binding site 5 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 5 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1584

b:14.4
occ:1.00
 O4 D:OXL1582 2.6 22.1 1.0
OG1 D:THR113 2.7 15.4 1.0
ND2 D:ASN466 2.8 14.4 1.0
ND2 D:ASN421 3.2 5.2 1.0
CE2 D:TYR112 3.4 17.3 1.0
OH D:TYR112 3.4 15.0 1.0
CZ D:TYR112 3.4 16.8 1.0
C2 D:OXL1582 3.5 18.7 1.0
OD1 D:ASN466 3.5 12.8 1.0
CG D:ASN466 3.6 13.7 1.0
O1 D:OXL1582 3.7 15.7 1.0
CB D:THR113 3.8 14.1 1.0
CG D:ASN421 3.9 8.0 1.0
C1 D:OXL1582 4.0 16.2 1.0
CD2 D:TYR112 4.2 17.0 1.0
CE1 D:TYR112 4.2 16.2 1.0
CD2 D:LEU167 4.4 8.7 1.0
O2 D:OXL1582 4.4 20.0 1.0
OD1 D:ASN421 4.4 5.7 1.0
CB D:ASN421 4.5 10.8 1.0
CG2 D:THR113 4.6 13.6 1.0
NZ D:LYS183 4.7 8.0 1.0
O D:HOH2049 4.9 12.1 1.0
CD1 D:TYR112 4.9 17.4 1.0
ND2 D:ASN467 4.9 18.9 1.0
CG D:TYR112 4.9 18.2 1.0
O D:GLY446 4.9 12.9 1.0
CA D:THR113 5.0 14.1 1.0
N D:THR113 5.0 13.9 1.0
CB D:ASN466 5.0 12.9 1.0

Sodium binding site 6 out of 36 in 1gq2

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Sodium binding site 6 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na1585

b:14.8
occ:1.00
 OE1 D:GLN64 2.9 9.3 1.0
N D:MSE38 3.1 17.2 1.0
CE D:MSE38 3.8 29.8 1.0
CB D:MSE38 3.8 20.2 1.0
CD D:GLN64 3.8 6.3 1.0
CA D:GLY37 3.9 16.1 1.0
CG D:GLN64 4.0 5.5 1.0
C D:GLY37 4.0 17.9 1.0
CA D:MSE38 4.0 17.6 1.0
CG D:MSE38 4.1 23.2 1.0
CD1 D:LEU59 4.2 21.0 1.0
O D:LYS36 4.4 15.4 1.0
SE D:MSE38 4.8 32.3 1.0
C D:MSE38 4.8 16.5 1.0
N D:ALA39 4.8 15.1 1.0
N D:GLY37 5.0 15.4 1.0
CB D:GLN64 5.0 9.2 1.0

Sodium binding site 7 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 7 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1584

b:11.9
occ:1.00
 O F:HOH2072 2.9 8.4 1.0
OG1 F:THR539 3.1 20.3 1.0
CD1 F:LEU483 3.6 14.4 1.0
ND2 F:ASN537 3.7 29.7 1.0
CA F:ALA534 4.1 23.9 1.0
OD2 F:ASP489 4.1 34.4 1.0
O F:GLU533 4.2 25.4 1.0
CB F:THR539 4.2 21.4 1.0
N F:ALA534 4.3 24.1 1.0
CG2 F:VAL490 4.3 14.6 1.0
C F:GLU533 4.3 25.4 1.0
CG2 F:THR539 4.5 20.7 1.0
CD2 F:LEU483 4.5 14.5 1.0
CB F:GLU533 4.6 28.4 1.0
CB F:ASN537 4.6 28.4 1.0
CG F:ASN537 4.7 30.1 1.0
CG F:LEU483 4.7 14.7 1.0
CB F:ALA534 4.7 24.2 1.0
OD1 F:ASP489 5.0 34.6 1.0

Sodium binding site 8 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 8 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na1585

b:12.5
occ:1.00
 O F:ARG129 2.7 15.0 1.0
OD2 F:ASP90 3.3 20.5 1.0
CB F:ARG131 3.4 15.0 1.0
CE F:MSE86 3.8 25.9 1.0
C F:ARG129 3.8 13.1 1.0
OD1 F:ASP90 3.9 19.6 1.0
CG F:ASP90 4.0 18.4 1.0
C F:PRO130 4.1 12.7 1.0
N F:ARG131 4.1 13.1 1.0
CD F:ARG131 4.3 18.5 1.0
O F:PRO130 4.3 11.8 1.0
CG F:ARG131 4.4 17.1 1.0
CA F:ARG131 4.4 14.4 1.0
CA F:PRO130 4.6 12.2 1.0
NH1 F:ARG131 4.6 23.2 1.0
N F:PRO130 4.6 13.0 1.0
N F:ARG129 4.6 12.8 1.0
CA F:ARG129 4.7 12.5 1.0
CB F:ARG129 4.8 12.3 1.0
O F:HOH2016 4.9 18.1 1.0
OH F:TYR123 5.0 11.3 1.0

Sodium binding site 9 out of 36 in 1gq2

Go back to Sodium Binding Sites List in 1gq2
Sodium binding site 9 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Na1584

b:18.2
occ:1.00
 O G:LEU29 2.8 14.4 1.0
O G:ARG91 3.1 11.4 1.0
C G:ARG30 3.2 17.4 1.0
NH2 H:ARG129 3.2 17.5 1.0
O G:ARG30 3.3 18.4 1.0
CA G:ARG30 3.4 17.6 1.0
N G:PRO32 3.5 15.7 1.0
CA G:ARG91 3.6 12.6 1.0
N G:ASP31 3.6 17.4 1.0
C G:ASP31 3.7 16.3 1.0
C G:ARG91 3.7 12.5 1.0
O G:ASP90 3.7 14.6 1.0
C G:LEU29 3.7 14.6 1.0
CD G:PRO32 3.8 15.6 1.0
CA G:PRO32 3.8 15.2 1.0
OD1 G:ASN35 4.0 14.4 1.0
N G:ARG30 4.0 16.1 1.0
CB G:ASN35 4.1 13.8 1.0
O G:ASP31 4.1 17.4 1.0
CZ H:ARG129 4.1 16.8 1.0
CB G:PRO32 4.1 14.9 1.0
CA G:ASP31 4.2 16.8 1.0
NE H:ARG129 4.3 13.2 1.0
CG G:ASN35 4.4 13.8 1.0
CB G:ARG91 4.5 13.8 1.0
CG G:ARG91 4.5 13.7 1.0
C G:ASP90 4.5 14.7 1.0
N G:ARG91 4.5 13.5 1.0
CG G:PRO32 4.6 14.2 1.0
CB G:ARG30 4.8 19.5 1.0
N G:ASN92 5.0 12.1 1.0

Sodium binding site 10 out of 36 in 1gq2

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Sodium binding site 10 out of 36 in the Malic Enzyme From Pigeon Liver


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Malic Enzyme From Pigeon Liver within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na1584

b:15.2
occ:1.00
 O H:THR113 2.9 17.6 1.0
NE2 H:GLN464 2.9 10.6 1.0
CE H:MSE108 3.1 24.8 1.0
CD H:PRO448 3.7 12.7 1.0
CD H:GLN464 3.7 12.6 1.0
OE1 H:GLN464 3.7 9.5 1.0
CG H:PRO448 3.8 12.7 1.0
C H:THR113 3.9 15.8 1.0
CG H:MSE108 4.0 20.1 1.0
CD2 H:TYR112 4.0 12.1 1.0
O H:MSE108 4.2 13.0 1.0
CA H:PRO109 4.2 14.1 1.0
N H:PRO109 4.2 13.7 1.0
C H:MSE108 4.2 13.7 1.0
N H:THR113 4.3 14.3 1.0
SE H:MSE108 4.3 28.9 1.0
CB H:THR113 4.3 15.1 1.0
CB H:MSE108 4.4 17.0 1.0
CA H:THR113 4.4 14.7 1.0
CB H:PRO448 4.5 13.1 1.0
CG H:PRO109 4.6 13.8 1.0
CB H:TYR112 4.6 13.1 1.0
CD H:PRO109 4.7 14.9 1.0
CG H:TYR112 4.8 13.8 1.0
N H:PRO448 4.9 13.0 1.0
CB H:PRO109 4.9 13.8 1.0
CE2 H:TYR112 4.9 12.0 1.0
C H:TYR112 4.9 14.1 1.0
OG1 H:THR113 4.9 17.2 1.0
CA H:MSE108 5.0 15.0 1.0

Reference:

Z.Yang, H.Zhang, H.-C.Huang, C.-C.Kuo, L.-C.Tsai, H.S.Yuan, W.-Y.Chou, G.-G.Chang, L.Tong. Structural Studies of the Pigeon Cytosolic Nadp+ -Dependent Malic Enzyme Protein Sci. V. 11 332 2002.
ISSN: ISSN 0961-8368
PubMed: 11790843
DOI: 10.1110/PS.38002
Page generated: Sun Oct 6 18:38:08 2024

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