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Sodium in PDB 3iqz: Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin

Enzymatic activity of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin

All present enzymatic activity of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin:
1.5.99.9;

Protein crystallography data

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin, PDB code: 3iqz was solved by K.E.Ceh, U.Demmer, E.Warkentin, J.Moll, R.K.Thauer, S.Shima, U.Ermler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 94.00 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 62.810, 167.700, 95.860, 90.00, 101.25, 90.00
R / Rfree (%) 19.8 / 22.6

Other elements in 3iqz:

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin (pdb code 3iqz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin, PDB code: 3iqz:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3iqz

Go back to Sodium Binding Sites List in 3iqz
Sodium binding site 1 out of 3 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na285

b:45.7
occ:0.90
 O D:HOH290 2.9 8.4 1.0
NH1 A:ARG263 3.0 2.5 1.0
O A:HOH288 3.1 17.0 1.0
CE1 B:TYR198 3.4 2.0 1.0
OE2 D:GLU136 3.5 9.0 1.0
CE1 D:PHE131 3.5 2.0 1.0
CE A:LYS256 3.5 5.1 1.0
CZ A:ARG263 3.9 4.3 1.0
CZ D:PHE131 3.9 2.0 1.0
NH2 A:ARG263 4.0 2.3 1.0
CD1 B:TYR198 4.1 2.0 1.0
NZ A:LYS256 4.1 4.4 1.0
CD D:GLU136 4.2 7.8 1.0
CZ B:TYR198 4.3 2.8 1.0
OE1 D:GLU239 4.4 7.2 1.0
OH B:TYR198 4.5 2.1 1.0
OE1 D:GLU136 4.5 9.1 1.0
CD A:LYS256 4.6 3.2 1.0
CD1 D:PHE131 4.6 2.1 1.0
NH1 A:ARG252 4.9 6.2 1.0
NE A:ARG252 4.9 10.6 1.0
CG A:LYS256 4.9 4.4 1.0

Sodium binding site 2 out of 3 in 3iqz

Go back to Sodium Binding Sites List in 3iqz
Sodium binding site 2 out of 3 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na285

b:73.0
occ:1.00
 C11 E:H4M284 4.1 41.1 1.0
C16 E:H4M284 4.2 39.0 1.0
C12 E:H4M284 4.2 38.2 1.0
CX1 E:H4M284 4.4 41.1 1.0
C15 E:H4M284 4.5 37.3 1.0
C13 E:H4M284 4.5 37.9 1.0
C14 E:H4M284 4.7 34.3 1.0

Sodium binding site 3 out of 3 in 3iqz

Go back to Sodium Binding Sites List in 3iqz
Sodium binding site 3 out of 3 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methylene-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Na285

b:58.5
occ:1.00
 NH2 F:ARG129 3.5 12.8 1.0
CD F:ARG129 3.6 9.9 1.0
CG F:ARG129 3.8 7.6 1.0
CB F:ARG129 3.9 5.7 1.0
CG F:GLU130 4.0 4.9 1.0
CD F:GLU130 4.1 5.6 1.0
CG B:PRO282 4.1 11.0 1.0
CD B:PRO282 4.2 11.2 1.0
OE1 F:GLU130 4.2 7.3 1.0
O1A F:H4M284 4.3 77.5 1.0
CZ F:ARG129 4.5 11.8 1.0
NE F:ARG129 4.5 10.9 1.0
OE2 F:GLU130 4.6 5.0 1.0
N F:GLU130 4.6 4.2 1.0
C3J F:H4M284 4.8 50.8 1.0
O5J F:H4M284 4.8 68.8 1.0
C F:ARG129 4.8 5.0 1.0
CA F:ARG129 5.0 5.7 1.0

Reference:

K.Ceh, U.Demmer, E.Warkentin, J.Moll, R.K.Thauer, S.Shima, U.Ermler. Structural Basis of the Hydride Transfer Mechanism in F(420)-Dependent Methylenetetrahydromethanopterin Dehydrogenase Biochemistry V. 48 10098 2009.
ISSN: ISSN 0006-2960
PubMed: 19761261
DOI: 10.1021/BI901104D
Page generated: Tue Dec 15 06:15:16 2020

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