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Sodium in PDB 5ou5: Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme

Protein crystallography data

The structure of Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme, PDB code: 5ou5 was solved by A.Bovdilova, A.Hoeppner, V.G.Maurino, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.88 / 2.20
Space group I 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 135.961, 147.155, 261.615, 90.00, 90.00, 90.00
R / Rfree (%) 16 / 21.1

Other elements in 5ou5:

The structure of Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Sodium atom in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme (pdb code 5ou5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 16 binding sites of Sodium where determined in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme, PDB code: 5ou5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 16 in 5ou5

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Sodium binding site 1 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na701

b:41.3
occ:1.00
O A:ALA334 2.8 31.3 1.0
ND2 A:ASN349 3.0 30.3 1.0
CD2 A:PHE326 3.4 41.0 1.0
CG A:PHE326 3.5 30.7 1.0
CB A:PHE326 3.5 30.7 1.0
CB A:ASN349 3.6 27.9 1.0
C A:ALA334 3.6 34.0 1.0
CA A:ALA334 3.7 30.6 1.0
CB A:LEU337 3.7 36.4 1.0
N A:LEU338 3.8 26.9 1.0
CG A:ASN349 3.8 32.0 1.0
CB A:LEU338 4.1 31.9 1.0
CE2 A:PHE326 4.1 43.6 1.0
CB A:ALA334 4.2 30.1 1.0
CA A:LEU338 4.2 30.2 1.0
CD1 A:PHE326 4.3 36.7 1.0
C A:LEU337 4.3 30.4 1.0
CA A:LEU337 4.5 31.8 1.0
CD1 A:LEU338 4.6 42.6 1.0
CA A:ASN349 4.7 27.3 1.0
CG A:LEU337 4.7 42.0 1.0
CD1 A:LEU337 4.8 48.1 1.0
O A:ASN333 4.8 34.0 1.0
CZ A:PHE326 4.9 38.9 1.0
CG A:LEU338 4.9 43.6 1.0
CE1 A:PHE326 4.9 39.7 1.0
N A:ALA334 4.9 31.4 1.0
N A:PHE335 4.9 36.8 1.0
N A:LEU337 5.0 32.6 1.0
OD1 A:ASN349 5.0 31.8 1.0

Sodium binding site 2 out of 16 in 5ou5

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Sodium binding site 2 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na702

b:55.6
occ:1.00
OG A:SER208 2.8 33.3 1.0
CB A:SER208 3.7 34.1 1.0
CB B:PRO128 3.8 30.0 1.0
CB A:LYS210 3.8 40.6 0.5
CB A:LYS210 4.0 40.3 0.5
CG B:PRO128 4.0 30.8 1.0
NH2 B:ARG123 4.0 80.8 1.0
O A:HOH819 4.0 42.5 1.0
CA B:PRO128 4.0 29.9 1.0
OD1 A:ASP211 4.2 46.3 1.0
O B:HOH819 4.4 51.3 1.0
OD2 A:ASP211 4.4 42.9 1.0
NE B:ARG123 4.4 71.1 1.0
CZ B:ARG123 4.5 82.2 1.0
CE A:LYS210 4.5 47.0 0.5
CG A:LYS210 4.6 43.4 0.5
CD2 A:LEU293 4.6 35.8 1.0
CG A:LYS210 4.6 42.2 0.5
CG A:ASP211 4.7 40.7 1.0
CA A:LYS210 4.8 38.5 0.5
CA A:LYS210 4.9 38.5 0.5
N B:PRO128 4.9 28.8 1.0
CD A:LYS210 4.9 44.3 0.5
CA A:SER208 4.9 29.7 1.0
O B:PRO128 4.9 34.4 1.0
CD B:PRO128 4.9 30.4 1.0

Sodium binding site 3 out of 16 in 5ou5

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Sodium binding site 3 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na703

b:44.6
occ:1.00
O A:HOH981 2.5 31.4 1.0
OH A:TYR635 2.9 35.7 1.0
N A:ARG633 3.2 30.8 1.0
CZ A:TYR635 3.4 32.8 1.0
CE2 A:TYR635 3.6 32.1 1.0
NE A:ARG166 3.8 47.6 1.0
CB A:ARG633 3.8 34.2 0.7
CA A:TYR632 3.8 28.4 1.0
O A:HOH807 3.8 40.4 1.0
CD A:ARG166 3.8 38.3 1.0
CB A:ARG633 3.8 32.7 0.3
CG A:ARG633 3.9 33.9 0.7
CA A:ARG633 3.9 32.4 0.7
CD1 A:TYR632 3.9 29.7 1.0
O A:ARG633 4.0 29.6 1.0
CA A:ARG633 4.0 31.4 0.3
C A:TYR632 4.0 27.8 1.0
CB A:TYR632 4.1 28.1 1.0
CG A:LYS108 4.2 29.9 1.0
C A:ARG633 4.4 31.9 1.0
CD A:LYS108 4.4 28.9 1.0
CE1 A:TYR635 4.5 31.8 1.0
CG A:TYR632 4.5 28.5 1.0
CZ A:ARG166 4.5 52.2 1.0
CG A:ARG166 4.5 33.1 1.0
O A:HIS106 4.6 30.3 1.0
O A:HIS105 4.7 33.0 1.0
CD2 A:TYR635 4.8 33.2 1.0
CG A:ARG633 4.8 32.6 0.3
NH2 A:ARG166 4.9 45.3 1.0
CE1 A:TYR632 4.9 28.1 1.0
CD A:ARG633 5.0 37.0 0.7
CD A:ARG633 5.0 33.3 0.3
CA A:HIS106 5.0 28.6 1.0
O A:HOH897 5.0 26.0 1.0

Sodium binding site 4 out of 16 in 5ou5

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Sodium binding site 4 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na701

b:37.7
occ:1.00
OH B:TYR98 2.5 43.6 1.0
O A:GLY204 2.6 26.5 1.0
O B:LEU125 2.8 22.6 1.0
CZ B:TYR98 3.6 41.3 1.0
C B:LEU125 3.6 25.5 1.0
CA B:LEU125 3.6 24.8 1.0
CB A:PRO202 3.6 39.2 1.0
C A:GLN203 3.7 27.8 1.0
C A:GLY204 3.7 27.1 1.0
N A:GLN203 3.7 26.4 1.0
C A:PRO202 3.7 30.5 1.0
N A:GLY204 3.7 25.5 1.0
CA A:GLN203 3.9 27.7 1.0
O A:PRO202 4.0 30.5 1.0
CB B:LEU125 4.0 24.4 1.0
CZ3 A:TRP222 4.0 28.9 1.0
O A:GLN203 4.1 32.2 1.0
CE2 B:TYR98 4.2 41.8 1.0
CA A:PRO202 4.3 36.7 1.0
CA A:GLY204 4.3 27.4 1.0
CE1 B:TYR98 4.5 40.1 1.0
CD2 B:LEU125 4.5 26.9 1.0
CH2 A:TRP222 4.7 26.6 1.0
O B:GLY124 4.7 27.8 1.0
O A:HOH929 4.8 43.6 1.0
N A:LEU205 4.8 25.9 1.0
N B:LEU126 4.8 26.0 1.0
CG B:LEU125 4.9 27.0 1.0
N B:LEU125 4.9 25.2 1.0
CG A:PRO202 5.0 40.3 1.0

Sodium binding site 5 out of 16 in 5ou5

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Sodium binding site 5 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na702

b:46.0
occ:1.00
O B:HOH885 2.8 29.8 1.0
OE1 B:GLN161 3.2 34.0 1.0
O B:VAL253 3.4 26.8 1.0
CB B:ALA257 3.4 27.5 1.0
CG1 B:VAL253 3.6 30.4 1.0
CE B:MET158 3.6 35.7 1.0
SD B:MET158 3.7 36.4 1.0
C B:VAL253 3.8 29.3 1.0
CD B:GLN161 3.8 31.9 1.0
NE2 B:GLN161 3.8 29.4 1.0
CA B:GLY254 3.9 29.9 1.0
N B:GLY254 4.1 31.4 1.0
O B:HOH880 4.2 29.2 1.0
CZ B:PHE168 4.2 27.2 1.0
O B:HOH811 4.4 36.3 1.0
CE2 B:PHE168 4.6 27.9 1.0
CB B:VAL253 4.7 26.3 1.0
CA B:ALA257 4.7 28.8 1.0
O B:GLY254 4.7 29.5 1.0
C B:GLY254 4.8 29.9 1.0
CA B:VAL253 4.8 27.6 1.0
N B:ALA257 4.9 26.6 1.0

Sodium binding site 6 out of 16 in 5ou5

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Sodium binding site 6 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na703

b:45.9
occ:1.00
O B:TYR539 2.7 37.5 1.0
OG B:SER593 2.8 34.3 1.0
N B:GLY543 3.0 33.9 1.0
C B:TYR539 3.4 32.4 1.0
CA B:SER593 3.6 30.7 1.0
CB B:SER593 3.6 31.2 1.0
CA B:GLY543 3.6 34.0 1.0
O B:ILE540 3.6 31.6 1.0
CD1 B:ILE596 3.7 38.2 1.0
CD B:PRO542 3.7 35.3 1.0
C B:ILE540 3.9 33.9 1.0
N B:PRO542 3.9 30.6 1.0
CB B:PRO542 3.9 33.3 1.0
N B:ILE540 4.0 36.8 1.0
C B:PRO542 4.0 30.0 1.0
CA B:ILE540 4.0 31.9 1.0
N B:SER593 4.1 30.6 1.0
CG B:PRO542 4.1 35.1 1.0
O B:ALA538 4.2 39.7 1.0
CA B:PRO542 4.2 32.0 1.0
CD1 B:ILE589 4.4 44.0 1.0
CG2 B:ILE592 4.4 43.9 1.0
CA B:TYR539 4.5 36.0 1.0
CB B:ILE596 4.6 30.5 1.0
CG1 B:ILE596 4.6 33.1 1.0
C B:ILE592 4.6 31.2 1.0
C B:GLY543 4.7 32.8 1.0
N B:PHE541 4.7 32.1 1.0
C B:PHE541 4.8 32.0 1.0
C B:SER593 4.8 29.6 1.0
N B:LEU544 4.8 30.9 1.0
CG2 B:ILE596 4.8 29.0 1.0
O B:ILE592 4.8 34.6 1.0
O B:ILE589 5.0 36.6 1.0
O B:SER593 5.0 28.1 1.0

Sodium binding site 7 out of 16 in 5ou5

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Sodium binding site 7 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na704

b:45.2
occ:1.00
OE1 B:GLU165 2.3 44.6 1.0
OH B:TYR628 2.6 33.2 1.0
O B:HOH859 2.7 40.7 1.0
CD B:GLU165 3.3 55.7 1.0
CZ B:TYR628 3.4 33.8 1.0
CE1 B:TYR628 3.5 35.2 1.0
NE B:ARG166 3.7 46.4 1.0
CG B:PRO267 3.7 36.2 1.0
CG B:GLU165 3.8 45.4 1.0
ND1 B:HIS105 3.8 46.9 1.0
CG B:ARG166 3.8 36.6 1.0
NH2 B:ARG166 3.9 38.6 1.0
CZ B:ARG166 4.0 42.4 1.0
CE1 B:HIS105 4.1 44.8 1.0
CD B:PRO267 4.3 31.6 1.0
CD B:ARG166 4.4 39.7 1.0
OE2 B:GLU165 4.4 58.1 1.0
CB B:GLU165 4.5 39.2 1.0
CE2 B:TYR628 4.7 35.9 1.0
CD1 B:TYR628 4.7 34.8 1.0
NH1 B:ARG166 4.9 38.3 1.0
O B:HIS105 4.9 30.5 1.0
CG B:HIS105 4.9 39.5 1.0
N B:ARG166 5.0 32.0 1.0

Sodium binding site 8 out of 16 in 5ou5

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Sodium binding site 8 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na705

b:46.5
occ:1.00
O B:SER491 2.7 42.0 1.0
OG B:SER497 2.9 47.5 1.0
OG B:SER518 2.9 62.1 1.0
O B:SER489 3.1 42.4 1.0
N B:SER518 3.2 59.5 1.0
N B:GLY517 3.3 41.9 1.0
CB B:SER497 3.4 49.1 1.0
CA B:GLY517 3.7 48.2 1.0
CB B:SER518 3.7 67.4 1.0
C B:SER491 3.7 49.6 1.0
CB B:SER516 3.8 44.9 1.0
C B:GLY517 3.9 56.0 1.0
CA B:SER497 3.9 45.9 1.0
CA B:SER518 4.1 64.5 1.0
C B:SER489 4.1 46.2 1.0
C B:LEU490 4.1 43.8 1.0
N B:SER491 4.1 46.5 1.0
C B:SER516 4.2 42.7 1.0
OG B:SER516 4.2 46.2 1.0
O B:LEU490 4.3 44.4 1.0
OG B:SER489 4.3 51.9 1.0
OD1 B:ASN492 4.3 67.8 1.0
CA B:SER516 4.4 41.6 1.0
CE2 B:PHE520 4.4 43.8 1.0
CA B:SER491 4.6 49.0 1.0
CA B:LEU490 4.6 42.9 1.0
N B:ASN492 4.6 51.6 1.0
N B:LEU490 4.7 39.5 1.0
N B:SER497 4.7 47.2 1.0
O B:PRO493 4.8 50.2 1.0
O B:SER518 4.8 58.3 1.0
CA B:ASN492 4.9 56.0 1.0
C B:SER518 4.9 67.7 1.0
CZ B:PHE520 5.0 44.0 1.0

Sodium binding site 9 out of 16 in 5ou5

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Sodium binding site 9 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na701

b:37.7
occ:1.00
O C:TYR539 2.8 28.6 1.0
OG C:SER593 2.8 29.1 1.0
N C:GLY543 2.9 32.8 1.0
C C:TYR539 3.5 32.9 1.0
CA C:GLY543 3.6 29.7 1.0
O C:ILE540 3.6 24.4 1.0
CD C:PRO542 3.7 30.9 1.0
CA C:SER593 3.7 28.5 1.0
CB C:SER593 3.7 27.6 1.0
CD1 C:ILE596 3.8 29.5 1.0
CB C:PRO542 3.9 31.1 1.0
C C:ILE540 3.9 28.1 1.0
N C:PRO542 3.9 26.7 1.0
C C:PRO542 3.9 31.0 1.0
CA C:ILE540 4.0 29.4 1.0
CG C:PRO542 4.0 32.7 1.0
N C:ILE540 4.0 30.7 1.0
CA C:PRO542 4.1 30.9 1.0
N C:SER593 4.2 31.0 1.0
O C:ALA538 4.2 33.0 1.0
CD1 C:ILE589 4.4 41.5 1.0
CA C:TYR539 4.5 31.8 1.0
C C:GLY543 4.7 31.0 1.0
N C:PHE541 4.7 28.2 1.0
CG2 C:ILE592 4.7 34.6 1.0
C C:PHE541 4.7 29.2 1.0
C C:ILE592 4.7 31.3 1.0
CB C:ILE596 4.8 25.9 1.0
N C:LEU544 4.8 32.0 1.0
CG1 C:ILE596 4.8 27.2 1.0
C C:SER593 4.9 29.2 1.0
O C:ILE592 4.9 32.1 1.0
O C:ILE589 4.9 33.9 1.0
CG1 C:ILE589 5.0 38.8 1.0
CG2 C:ILE596 5.0 26.6 1.0
O C:SER593 5.0 31.3 1.0

Sodium binding site 10 out of 16 in 5ou5

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Sodium binding site 10 out of 16 in the Crystal Structure of Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme


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 Maize Chloroplastic Photosynthetic Nadp(+)- Dependent Malic Enzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na702

b:55.0
occ:1.00
OG C:SER497 2.7 41.3 1.0
O C:SER489 2.8 35.8 1.0
O C:SER491 2.9 51.7 1.0
OG C:SER518 2.9 42.6 0.4
N C:SER518 3.3 42.7 1.0
CB C:SER497 3.3 37.6 1.0
N C:GLY517 3.4 33.3 1.0
CB C:SER516 3.5 36.7 1.0
CB C:SER518 3.6 45.1 0.4
CB C:SER518 3.9 52.7 0.6
C C:SER489 3.9 35.5 1.0
CA C:SER497 3.9 37.4 1.0
C C:SER491 4.0 46.9 1.0
CA C:GLY517 4.0 35.4 1.0
CA C:SER518 4.0 46.3 0.4
C C:GLY517 4.1 46.2 1.0
CA C:SER518 4.1 49.1 0.6
C C:SER516 4.1 30.9 1.0
CA C:SER516 4.1 35.3 1.0
C C:LEU490 4.2 40.3 1.0
N C:SER491 4.3 42.4 1.0
OG C:SER516 4.3 43.3 1.0
CE2 C:PHE520 4.4 40.6 1.0
CB C:SER489 4.4 35.6 1.0
OG C:SER518 4.4 47.9 0.6
O C:LEU490 4.5 40.7 1.0
CA C:LEU490 4.6 37.1 1.0
O C:SER518 4.6 48.1 1.0
N C:LEU490 4.6 35.0 1.0
CA C:SER491 4.7 45.9 1.0
N C:SER497 4.7 40.6 1.0
CZ C:PHE520 4.8 38.5 1.0
C C:SER518 4.8 48.8 1.0
CA C:SER489 4.8 35.3 1.0
N C:ASN492 4.8 52.4 1.0
OD1 C:ASN492 5.0 79.2 1.0

Reference:

C.E.Alvarez, A.Bovdilova, A.Hoppner, C.C.Wolff, M.Saigo, F.Trajtenberg, T.Zhang, A.Buschiazzo, L.Nagel-Steger, M.F.Drincovich, M.J.Lercher, V.G.Maurino. Molecular Adaptations of Nadp-Malic Enzyme For Its Function in C4PHOTOSYNTHESIS in Grasses. Nat.Plants V. 5 755 2019.
ISSN: ESSN 2055-0278
PubMed: 31235877
DOI: 10.1038/S41477-019-0451-7
Page generated: Tue Dec 15 11:25:55 2020

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