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Calcium in PDB 3iqf: Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin

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

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

Protein crystallography data

The structure of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin, PDB code: 3iqf 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) 112.50 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 103.400, 167.100, 122.500, 90.00, 113.60, 90.00
R / Rfree (%) 16 / 20

Other elements in 3iqf:

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

Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin (pdb code 3iqf). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin, PDB code: 3iqf:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 3iqf

Go back to Calcium Binding Sites List in 3iqf
Calcium binding site 1 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca285

b:98.6
occ:1.00
 O B:HOH1188 3.5 49.1 1.0
O B:HOH1202 4.4 45.2 1.0
OE1 B:GLU175 4.6 50.6 1.0
O B:GLN112 4.8 27.7 1.0
O B:ALA88 4.8 24.8 1.0
O B:HOH290 4.8 50.4 1.0

Calcium binding site 2 out of 7 in 3iqf

Go back to Calcium Binding Sites List in 3iqf
Calcium binding site 2 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca285

b:28.0
occ:1.00
 OE2 E:GLU50 2.0 29.1 1.0
OE1 E:GLU47 2.4 36.2 1.0
OE2 E:GLU47 2.5 38.8 1.0
CD E:GLU47 2.8 35.4 1.0
CD E:GLU50 2.8 32.8 1.0
OE1 E:GLU50 3.1 35.8 1.0
O E:HOH450 4.0 44.5 1.0
CG E:GLU50 4.2 31.2 1.0
CG E:GLU47 4.3 32.1 1.0
CB E:GLU50 4.6 28.2 1.0
CA E:GLU47 4.8 26.9 1.0

Calcium binding site 3 out of 7 in 3iqf

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Calcium binding site 3 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca285

b:52.4
occ:1.00
 O I:ARG129 2.8 22.1 1.0
CG K:PRO265 3.3 22.7 1.0
C I:PHE131 3.3 21.3 1.0
O I:PHE131 3.4 20.7 1.0
CD K:PRO265 3.4 21.9 1.0
CB K:ARG263 3.5 19.9 1.0
N I:ASP133 3.5 21.6 1.0
CB K:PRO265 3.6 22.6 1.0
N I:PHE131 3.6 21.3 1.0
CB I:ASP133 3.6 21.4 1.0
N I:LEU132 3.6 21.3 1.0
C I:GLU130 3.7 22.2 1.0
C I:LEU132 3.7 21.5 1.0
CD K:ARG263 3.8 21.3 1.0
O I:GLU130 3.8 22.4 1.0
CA I:PHE131 3.8 21.3 1.0
C I:ARG129 3.9 22.3 1.0
CA I:ASP133 4.0 21.4 1.0
O I:LEU132 4.0 21.9 1.0
CG K:ARG263 4.1 21.5 1.0
CA I:LEU132 4.2 21.7 1.0
N K:PRO265 4.3 21.9 1.0
CA I:GLU130 4.4 22.1 1.0
CG I:ASP133 4.5 23.0 1.0
CD K:LYS275 4.5 20.9 1.0
N I:GLU130 4.6 22.2 1.0
CA K:ARG263 4.6 19.2 1.0
CA K:PRO265 4.6 22.2 1.0
C K:ARG263 4.7 19.5 1.0
OD1 I:ASP133 4.8 21.5 1.0
N K:THR264 4.9 20.4 1.0
CA I:ARG129 5.0 22.7 1.0

Calcium binding site 4 out of 7 in 3iqf

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Calcium binding site 4 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca285

b:63.9
occ:1.00
 OD1 K:ASN258 3.0 29.4 1.0
OD1 J:ASN258 3.2 30.4 1.0
ND2 L:ASN258 3.2 29.7 1.0
O J:SER257 3.3 19.3 1.0
OG J:SER257 3.3 22.4 1.0
OG K:SER257 3.4 24.7 1.0
OG L:SER257 3.4 26.3 1.0
O L:SER257 3.5 20.2 1.0
O K:SER257 3.6 20.2 1.0
CB J:SER257 3.7 21.3 1.0
C J:SER257 3.7 20.8 1.0
CG K:ASN258 3.8 26.3 1.0
CB L:SER257 3.8 22.3 1.0
CB K:SER257 3.9 23.1 1.0
C L:SER257 3.9 21.2 1.0
CG J:ASN258 3.9 25.0 1.0
C K:SER257 3.9 21.6 1.0
CG L:ASN258 4.1 26.3 1.0
ND2 J:ASN258 4.2 27.4 1.0
ND2 K:ASN258 4.3 22.8 1.0
N J:ASN258 4.3 21.4 1.0
CA J:SER257 4.4 20.8 1.0
N L:ASN258 4.4 21.6 1.0
OD1 L:ASN258 4.4 26.1 1.0
N K:ASN258 4.4 21.3 1.0
CA L:SER257 4.5 21.5 1.0
CA K:SER257 4.5 21.5 1.0
CA J:ASN258 4.6 22.1 1.0
CA K:ASN258 4.7 22.6 1.0
CA L:ASN258 4.7 22.4 1.0
CB K:ASN258 4.9 23.3 1.0
CB J:ASN258 4.9 22.4 1.0

Calcium binding site 5 out of 7 in 3iqf

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Calcium binding site 5 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca285

b:30.0
occ:1.00
 OD2 K:ASP89 1.8 28.8 1.0
OE2 K:GLU85 1.8 22.5 1.0
CG K:ASP89 2.7 26.9 1.0
CD K:GLU85 2.8 19.2 1.0
OD1 K:ASP89 2.9 26.1 1.0
CG K:GLU85 3.3 20.9 1.0
OE1 K:GLU85 3.9 21.2 1.0
CB K:ASP89 4.1 25.2 1.0
O K:HOH310 4.5 47.1 1.0
O K:GLU85 4.6 20.7 1.0
CB K:GLU85 4.8 21.8 1.0

Calcium binding site 6 out of 7 in 3iqf

Go back to Calcium Binding Sites List in 3iqf
Calcium binding site 6 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca286

b:52.5
occ:1.00
 OD1 K:ASP259 2.6 23.1 1.0
O K:ARG276 2.6 26.4 1.0
OH L:TYR198 2.8 15.8 1.0
N K:VAL261 3.1 20.7 1.0
O K:HOH1233 3.1 23.8 1.0
CE2 L:TYR198 3.2 18.7 1.0
C K:ASP259 3.2 21.2 1.0
N K:ALA260 3.3 20.9 1.0
CZ L:TYR198 3.4 17.2 1.0
O K:ASP259 3.4 18.9 1.0
N K:PHE278 3.5 23.6 1.0
CA K:ASP259 3.6 20.9 1.0
CG K:ASP259 3.7 22.4 1.0
CB K:VAL261 3.7 20.8 1.0
C K:ARG276 3.8 25.1 1.0
CG2 K:VAL261 3.8 21.9 1.0
CA K:VAL261 3.9 19.9 1.0
C K:LYS277 3.9 24.5 1.0
CA K:ALA260 4.0 21.5 1.0
C K:ALA260 4.0 21.0 1.0
CA K:LYS277 4.0 25.1 1.0
CA K:PHE278 4.0 24.4 1.0
O K:VAL261 4.0 20.1 1.0
CB K:PHE278 4.2 24.2 1.0
CB K:ASP259 4.3 21.9 1.0
N K:LYS277 4.4 24.4 1.0
C K:VAL261 4.4 20.4 1.0
CD2 L:TYR198 4.5 16.0 1.0
OD2 K:ASP259 4.6 21.8 1.0
O K:LYS277 4.7 23.4 1.0
CE1 L:TYR198 4.7 19.4 1.0
N K:ASP259 4.9 22.0 1.0
CA K:ARG276 5.0 24.9 1.0

Calcium binding site 7 out of 7 in 3iqf

Go back to Calcium Binding Sites List in 3iqf
Calcium binding site 7 out of 7 in the Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Structure of F420 Dependent Methylene-Tetrahydromethanopterin Dehydrogenase in Complex with Methenyl-Tetrahydromethanopterin within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca285

b:55.7
occ:1.00
 O L:ARG276 2.6 26.9 1.0
OH J:TYR198 2.7 16.4 1.0
OD1 L:ASP259 2.8 24.1 1.0
O L:HOH1218 3.0 25.3 1.0
N L:VAL261 3.0 21.2 1.0
CE2 J:TYR198 3.2 18.2 1.0
C L:ASP259 3.3 21.1 1.0
N L:ALA260 3.3 21.0 1.0
CZ J:TYR198 3.4 16.0 1.0
N L:PHE278 3.6 24.6 1.0
O L:ASP259 3.6 20.5 1.0
CB L:VAL261 3.6 20.5 1.0
CA L:ASP259 3.7 21.1 1.0
C L:ARG276 3.7 25.4 1.0
CA L:VAL261 3.8 20.1 1.0
CG2 L:VAL261 3.8 21.4 1.0
O L:VAL261 3.9 19.9 1.0
C L:ALA260 3.9 21.4 1.0
CG L:ASP259 3.9 20.9 1.0
CA L:ALA260 3.9 21.3 1.0
C L:LYS277 4.0 24.5 1.0
CA L:LYS277 4.1 25.2 1.0
CA L:PHE278 4.1 24.6 1.0
C L:VAL261 4.3 20.6 1.0
CB L:PHE278 4.3 23.5 1.0
N L:LYS277 4.4 24.3 1.0
CB L:ASP259 4.4 22.9 1.0
CD2 J:TYR198 4.5 20.6 1.0
CE1 J:TYR198 4.7 17.1 1.0
OD2 L:ASP259 4.8 24.7 1.0
O L:LYS277 4.9 23.0 1.0
CA L:ARG276 4.9 25.0 1.0
N L:ASP259 4.9 21.9 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: Sat Jul 13 11:45:32 2024

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