Zinc in PDB 7mdh: Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form

Enzymatic activity of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form

All present enzymatic activity of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form:
1.1.1.82;

Protein crystallography data

The structure of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form, PDB code: 7mdh was solved by K.Johansson, S.Ramaswamy, M.Saarinen, M.Lemaire-Chamley, E.Issakidis-Bourguet, M.Miginiac-Maslow, H.Eklund, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.40
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 145.424, 153.944, 160.042, 90.00, 90.00, 90.00
R / Rfree (%) 22.1 / 27.1

Zinc Binding Sites:

Pages:

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

Binding sites:

The binding sites of Zinc atom in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form (pdb code 7mdh). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 17 binding sites of Zinc where determined in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form, PDB code: 7mdh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 17 in 7mdh

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Zinc binding site 1 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:86.8
occ:1.00
SG A:CYS175 1.5 63.0 1.0
ND1 A:HIS229 2.1 50.6 1.0
O A:HOH525 2.8 35.7 1.0
CG A:HIS229 2.8 51.9 1.0
CB A:CYS175 2.9 34.8 1.0
OD1 A:ASN173 2.9 46.8 1.0
CE1 A:HIS229 3.0 50.8 1.0
CB A:HIS229 3.2 42.7 1.0
O A:LEU197 3.5 30.7 1.0
CD2 A:HIS229 3.8 51.6 1.0
NE2 A:HIS229 3.9 53.1 1.0
CG A:ASN173 4.1 45.0 1.0
CA A:CYS175 4.1 37.4 1.0
N A:CYS175 4.1 31.4 1.0
O A:VAL171 4.2 25.2 1.0
ND2 A:ASN173 4.6 42.3 1.0
C A:LEU197 4.6 31.9 1.0
CA A:HIS229 4.7 42.4 1.0
C A:VAL171 4.9 33.1 1.0
O A:HIS229 4.9 36.5 1.0
N A:LEU197 4.9 32.1 1.0

Zinc binding site 2 out of 17 in 7mdh

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Zinc binding site 2 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:41.8
occ:1.00
OD2 A:ASP321 1.8 34.3 1.0
OE2 A:GLU372 2.0 46.8 1.0
NZ A:LYS363 2.0 53.0 1.0
CE A:LYS363 2.7 49.0 1.0
CG A:ASP321 3.0 37.7 1.0
CD A:GLU372 3.2 51.1 1.0
CB A:ASP321 3.5 30.3 1.0
O A:ASP321 3.9 41.3 1.0
OD1 A:ASP321 4.0 36.8 1.0
OE1 A:GLU372 4.1 55.2 1.0
CG A:GLU372 4.1 52.1 1.0
CD A:LYS363 4.1 47.7 1.0
NZ A:LYS184 4.4 50.3 1.0
CE A:LYS184 4.5 50.1 1.0
C A:ASP321 4.8 40.5 1.0
CA A:ASP321 4.8 36.2 1.0

Zinc binding site 3 out of 17 in 7mdh

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Zinc binding site 3 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:0.1
occ:1.00
NE2 A:HIS229 2.5 53.1 1.0
OD2 A:ASP201 2.6 32.9 1.0
O A:HOH524 2.9 37.9 1.0
CE1 A:HIS229 3.0 50.8 1.0
CD1 A:LEU385 3.2 44.2 1.0
OD1 A:ASP201 3.3 35.3 1.0
CG A:ASP201 3.3 32.7 1.0
CD2 A:HIS229 3.5 51.6 1.0
ND1 A:HIS229 4.1 50.6 1.0
CB A:LEU385 4.3 56.6 1.0
CG A:LEU385 4.3 52.3 1.0
CG A:HIS229 4.4 51.9 1.0
CD2 A:LEU200 4.4 27.4 1.0
NH1 A:ARG204 4.5 27.0 1.0
CB A:ASP201 4.7 30.5 1.0
CG A:LEU200 4.8 30.4 1.0
OE1 A:GLN233 4.8 51.1 1.0

Zinc binding site 4 out of 17 in 7mdh

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Zinc binding site 4 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:70.8
occ:1.00
OE2 A:GLU121 2.5 67.5 1.0
OE1 A:GLU121 2.6 57.3 1.0
OD1 A:ASP23 2.6 79.2 1.0
OD2 A:ASP23 2.6 80.3 1.0
OE1 A:GLU118 2.6 77.2 1.0
CD A:GLU121 2.7 63.9 1.0
CG A:ASP23 2.9 75.6 1.0
CD A:GLU118 3.2 71.2 1.0
OE2 A:GLU118 3.7 74.5 1.0
CG A:GLU121 4.0 56.2 1.0
CG A:GLU118 4.2 63.6 1.0
CB A:ASP23 4.4 66.3 1.0
O A:GLU118 4.4 39.2 1.0

Zinc binding site 5 out of 17 in 7mdh

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Zinc binding site 5 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:28.1
occ:1.00
O B:HOH512 1.7 16.5 1.0
OE2 B:GLU109 2.2 27.9 1.0
CD B:GLU109 2.9 29.9 1.0
OE1 B:GLU109 3.0 27.6 1.0
O B:HOH513 3.4 29.7 1.0
CD2 B:LEU46 4.1 27.4 1.0
CG B:GLU109 4.2 22.0 1.0

Zinc binding site 6 out of 17 in 7mdh

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Zinc binding site 6 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:50.0
occ:1.00
O B:HOH516 2.2 31.6 1.0
O B:HOH517 2.3 38.8 1.0
OD1 B:ASP122 2.5 33.5 1.0
CG B:ASP122 3.2 38.8 1.0
OD2 B:ASP122 3.3 49.0 1.0
O B:VAL161 3.7 28.7 1.0
O B:HOH515 4.3 63.9 1.0
N B:ASP122 4.4 19.6 1.0
CB B:ASP122 4.5 30.2 1.0
CA B:ASP122 4.6 26.9 1.0
C B:VAL161 4.8 32.8 1.0

Zinc binding site 7 out of 17 in 7mdh

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Zinc binding site 7 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:76.8
occ:1.00
NE2 B:HIS229 2.1 38.0 1.0
OD2 B:ASP201 2.3 23.8 1.0
CE1 B:HIS229 2.8 35.1 1.0
O B:HOH543 2.8 60.9 1.0
CG B:ASP201 3.1 22.1 1.0
OD1 B:ASP201 3.2 32.8 1.0
CD2 B:HIS229 3.2 31.8 1.0
CD1 B:LEU385 3.4 57.3 1.0
ND1 B:HIS229 4.0 33.8 1.0
O B:HOH544 4.1 34.3 1.0
CG B:HIS229 4.2 31.0 1.0
CB B:LEU385 4.3 68.2 1.0
CG B:LEU385 4.5 63.8 1.0
CD2 B:LEU200 4.5 22.5 1.0
CB B:ASP201 4.5 24.7 1.0
NH1 B:ARG204 4.7 22.4 1.0
OE1 B:GLN233 4.9 41.6 1.0

Zinc binding site 8 out of 17 in 7mdh

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Zinc binding site 8 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:61.7
occ:1.00
SG B:CYS175 1.7 60.8 1.0
ND1 B:HIS229 2.2 33.8 1.0
CB B:CYS175 2.7 26.5 1.0
CG B:HIS229 3.0 31.0 1.0
OD1 B:ASN173 3.1 48.0 1.0
CB B:HIS229 3.2 32.3 1.0
CE1 B:HIS229 3.3 35.1 1.0
N B:CYS175 3.9 25.9 1.0
CA B:CYS175 3.9 29.2 1.0
O B:VAL171 4.0 24.5 1.0
O B:LEU197 4.1 21.4 1.0
CD2 B:HIS229 4.2 31.8 1.0
CG B:ASN173 4.3 46.4 1.0
NE2 B:HIS229 4.3 38.0 1.0
C B:VAL171 4.7 23.4 1.0
CA B:HIS229 4.7 35.1 1.0
O B:HIS229 4.7 36.0 1.0
CA B:VAL171 4.9 19.5 1.0

Zinc binding site 9 out of 17 in 7mdh

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Zinc binding site 9 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:65.0
occ:1.00
OE2 B:GLU258 2.4 63.8 1.0
OE1 B:GLU258 2.6 58.7 1.0
CD B:GLU258 2.8 55.4 1.0
CG2 B:THR254 3.1 60.2 1.0
CG B:GLU258 4.2 49.9 1.0
CB B:THR254 4.5 59.7 1.0
OG1 B:THR254 4.9 64.4 1.0

Zinc binding site 10 out of 17 in 7mdh

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Zinc binding site 10 out of 17 in the Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structural Basis For Light Acitvation of A Chloroplast Enzyme. the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn501

b:65.0
occ:1.00
OE1 C:GLU93 2.4 32.7 1.0
OE2 C:GLU93 2.4 38.8 1.0
O D:HOH586 2.4 52.3 1.0
NE2 B:HIS368 2.6 59.8 1.0
CD C:GLU93 2.7 38.2 1.0
O B:HOH558 2.8 43.3 1.0
NZ D:LYS275 3.1 57.2 1.0
CD2 B:HIS368 3.3 60.5 1.0
CE1 B:HIS368 3.5 57.0 1.0
OE1 B:GLN149 3.9 48.6 1.0
CG C:GLU93 4.2 34.9 1.0
CG B:HIS368 4.4 56.6 1.0
CE D:LYS275 4.4 50.1 1.0
CG C:GLN90 4.5 46.4 1.0
ND1 B:HIS368 4.5 57.8 1.0
CD2 B:LEU369 4.6 32.4 1.0
CD B:GLN149 4.7 43.2 1.0
CE2 C:PHE89 4.7 30.9 1.0
CD2 C:PHE89 4.8 29.7 1.0
CD D:LYS275 4.8 52.5 1.0
NE2 B:GLN149 4.8 44.2 1.0

Reference:

K.Johansson, S.Ramaswamy, M.Saarinen, M.Lemaire-Chamley, E.Issakidis-Bourguet, M.Miginiac-Maslow, H.Eklund. Structural Basis For Light Activation of A Chloroplast Enzyme: the Structure of Sorghum Nadp-Malate Dehydrogenase in Its Oxidized Form. Biochemistry V. 38 4319 1999.
ISSN: ISSN 0006-2960
PubMed: 10194350
DOI: 10.1021/BI982876C
Page generated: Wed Dec 16 14:05:00 2020

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