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Calcium in PDB 5mki: Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii

Protein crystallography data

The structure of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii, PDB code: 5mki was solved by A.D.Nikulin, N.V.Lekontseva, S.V.Tishchenko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.16 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 69.671, 114.221, 71.993, 90.00, 113.70, 90.00
R / Rfree (%) 19.1 / 25.7

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii (pdb code 5mki). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 10 binding sites of Calcium where determined in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii, PDB code: 5mki:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 10 in 5mki

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Calcium binding site 1 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca101

b:41.0
occ:0.59
O C:HOH229 2.3 38.6 1.0
O C:ASN18 2.4 34.6 1.0
O C:HOH214 2.5 38.7 1.0
O C:HOH223 2.5 41.9 1.0
O C:HOH217 2.5 38.3 1.0
O C:HOH211 2.6 40.7 1.0
O C:LEU72 2.8 43.4 1.0
C C:ASN18 3.6 35.5 1.0
C C:LEU72 4.0 42.2 1.0
OG1 C:THR17 4.3 29.9 1.0
O C:HOH212 4.4 43.5 1.0
N C:ASN18 4.4 28.8 1.0
CA C:ASN18 4.5 31.2 1.0
CB C:THR17 4.6 31.9 1.0
N C:VAL19 4.6 34.3 1.0
CB C:ASN18 4.7 35.0 1.0
CA C:LEU72 4.7 34.5 1.0
CA C:VAL19 4.7 33.1 1.0
OXT C:LEU72 4.9 38.3 1.0

Calcium binding site 2 out of 10 in 5mki

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Calcium binding site 2 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Ca101

b:52.6
occ:0.74
O D:HOH228 2.7 34.0 1.0
ND2 D:ASN41 3.2 25.8 1.0
NH1 D:ARG63 3.4 34.4 1.0
OD1 D:ASN41 3.8 21.5 1.0
ND1 D:HIS39 3.8 38.4 1.0
O C:LEU38 3.8 31.2 1.0
CG D:HIS39 3.9 32.4 1.0
CG D:ASN41 3.9 24.5 1.0
O C:HOH225 4.0 40.2 1.0
CB D:HIS39 4.0 25.1 1.0
CZ D:ARG63 4.1 35.0 1.0
NH2 D:ARG63 4.4 40.0 1.0
CE1 D:HIS39 4.4 44.1 1.0
CD2 D:HIS39 4.6 33.0 1.0
O C:HIS39 4.8 23.2 1.0
CG D:ARG63 4.8 27.1 1.0
CG C:MET40 4.8 31.6 1.0
C C:HIS39 4.8 24.3 1.0
CA C:HIS39 4.9 23.3 1.0
NE2 D:HIS39 4.9 39.5 1.0
NE D:ARG63 4.9 36.5 1.0
C C:LEU38 5.0 29.4 1.0

Calcium binding site 3 out of 10 in 5mki

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Calcium binding site 3 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Ca101

b:53.1
occ:0.61
O E:HOH228 2.2 38.3 1.0
O E:HOH209 2.3 31.0 1.0
O E:HOH238 2.4 44.7 1.0
OD1 E:ASN41 3.6 22.3 1.0
NH1 E:ARG63 3.6 35.4 1.0
CZ E:ARG63 3.6 37.4 1.0
NH2 E:ARG63 3.7 33.7 1.0
CB E:HIS39 3.9 37.0 1.0
ND2 E:ASN41 3.9 25.5 1.0
CG E:HIS39 4.1 38.0 1.0
CG E:ARG63 4.2 32.4 1.0
CG E:ASN41 4.2 24.9 1.0
NE E:ARG63 4.2 35.9 1.0
OD1 E:ASP65 4.4 54.6 1.0
ND1 E:HIS39 4.6 39.4 1.0
CD2 E:HIS39 4.6 42.4 1.0
N E:GLY64 4.7 18.3 1.0
N E:ASP65 4.8 24.4 1.0
CD E:ARG63 4.8 33.0 1.0

Calcium binding site 4 out of 10 in 5mki

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Calcium binding site 4 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Ca101

b:55.6
occ:0.66
O F:HOH223 2.2 34.5 1.0
O F:HOH226 2.4 42.9 1.0
O F:HOH225 2.5 33.5 1.0
NH1 F:ARG63 3.3 32.0 1.0
CZ F:ARG63 3.8 33.2 1.0
CG F:HIS39 3.9 40.2 1.0
CB F:HIS39 4.1 32.1 1.0
NH2 F:ARG63 4.1 40.3 1.0
OD1 F:ASN41 4.2 26.4 1.0
CD2 F:HIS39 4.2 41.4 1.0
ND2 F:ASN41 4.2 27.4 1.0
ND1 F:HIS39 4.3 37.9 1.0
CG F:ASN41 4.6 26.3 1.0
NE F:ARG63 4.7 37.8 1.0
CG F:ARG63 4.7 27.8 1.0
NE2 F:HIS39 4.7 47.9 1.0
CE1 F:HIS39 4.7 48.6 1.0
O E:LEU38 4.8 37.3 1.0
O E:HOH207 5.0 36.7 1.0

Calcium binding site 5 out of 10 in 5mki

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Calcium binding site 5 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Ca101

b:38.6
occ:0.52
O G:HOH236 2.4 40.5 1.0
O G:ASN18 2.5 34.2 1.0
O G:HOH202 2.7 43.3 1.0
O G:LEU72 2.9 41.6 1.0
O G:HOH210 3.0 37.0 1.0
C G:ASN18 3.7 30.3 1.0
C G:LEU72 4.1 38.1 1.0
N G:ASN18 4.2 26.7 1.0
OG1 G:THR17 4.3 32.7 1.0
CA G:ASN18 4.4 34.2 1.0
O G:HOH229 4.5 32.0 1.0
CB G:ASN18 4.6 34.3 1.0
CB G:THR17 4.6 27.3 1.0
N G:VAL19 4.7 30.7 1.0
OXT G:LEU72 4.8 34.6 1.0
CA G:VAL19 4.9 28.4 1.0
CA G:LEU72 4.9 28.3 1.0

Calcium binding site 6 out of 10 in 5mki

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Calcium binding site 6 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Ca101

b:36.7
occ:0.48
O I:HOH228 2.1 32.4 1.0
O I:HOH222 2.2 33.5 1.0
O I:HOH235 2.3 45.2 1.0
OD1 I:ASN41 2.8 24.4 1.0
ND2 I:ASN41 3.1 26.9 1.0
CG I:ASN41 3.3 27.3 1.0
NH1 I:ARG63 3.5 32.2 1.0
CB I:HIS39 3.7 33.4 1.0
CZ I:ARG63 3.8 31.6 1.0
CG I:ARG63 3.9 28.3 1.0
CG I:HIS39 4.0 37.0 1.0
NH2 I:ARG63 4.2 43.2 1.0
ND1 I:HIS39 4.2 38.4 1.0
N I:GLY64 4.3 21.1 1.0
NE I:ARG63 4.3 33.5 1.0
CD I:ARG63 4.7 30.1 1.0
CB I:ASN41 4.8 20.3 1.0
CD2 I:HIS39 4.8 41.4 1.0
N I:ASP65 4.9 24.5 1.0
O I:HIS39 4.9 25.0 1.0
CA I:GLY64 4.9 24.3 1.0

Calcium binding site 7 out of 10 in 5mki

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Calcium binding site 7 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Ca101

b:45.5
occ:0.49
O I:HOH227 2.3 35.5 1.0
O J:HOH223 2.3 30.0 1.0
O J:HOH228 2.7 46.0 1.0
ND2 J:ASN41 3.2 25.4 1.0
OD1 J:ASN41 3.4 24.9 1.0
CB J:HIS39 3.5 31.7 1.0
CG J:HIS39 3.6 34.8 1.0
CG J:ASN41 3.7 27.1 1.0
NH2 J:ARG63 3.7 36.5 1.0
CD2 J:HIS39 4.0 38.5 1.0
CZ J:ARG63 4.1 35.9 1.0
ND1 J:HIS39 4.1 42.5 1.0
NH1 J:ARG63 4.2 35.4 1.0
O I:HOH212 4.5 38.0 1.0
NE2 J:HIS39 4.6 42.3 1.0
CG J:ARG63 4.7 30.0 1.0
CE1 J:HIS39 4.7 47.0 1.0
O I:LEU38 4.8 31.4 1.0
N J:GLY64 4.9 21.1 1.0
NE J:ARG63 4.9 35.9 1.0
O J:HOH232 4.9 51.2 1.0
CA J:HIS39 4.9 26.6 1.0

Calcium binding site 8 out of 10 in 5mki

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Calcium binding site 8 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 8 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Ca101

b:55.3
occ:0.84
ND2 K:ASN41 3.1 27.8 1.0
O K:HOH221 3.1 33.7 1.0
OD1 K:ASN41 3.1 21.9 1.0
CG K:ASN41 3.5 26.3 1.0
CZ K:ARG63 4.0 36.8 1.0
NE K:ARG63 4.0 36.9 1.0
NH2 K:ARG63 4.0 33.9 1.0
O J:LEU38 4.0 33.6 1.0
CG K:ARG63 4.1 27.6 1.0
CG K:HIS39 4.2 40.0 1.0
CB K:HIS39 4.2 31.1 1.0
CD2 K:HIS39 4.3 37.8 1.0
O J:HOH215 4.4 38.5 1.0
SD J:MET40 4.5 44.1 1.0
CG J:MET40 4.6 37.2 1.0
NH1 K:ARG63 4.6 33.3 1.0
CD K:ARG63 4.7 34.8 1.0
O J:HIS39 4.7 25.3 1.0
ND1 K:HIS39 4.8 44.1 1.0
C J:HIS39 4.8 28.9 1.0
NE2 K:HIS39 4.9 47.6 1.0
N K:GLY64 5.0 20.7 1.0

Calcium binding site 9 out of 10 in 5mki

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Calcium binding site 9 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 9 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Ca101

b:65.6
occ:1.00
O L:HOH229 2.3 44.4 1.0
O L:ASN18 2.3 35.9 1.0
O L:HOH225 2.3 47.5 1.0
O L:HOH204 2.5 37.3 1.0
O L:HOH216 2.7 36.5 1.0
OXT L:LEU72 3.2 44.5 1.0
C L:ASN18 3.5 35.0 1.0
C L:LEU72 4.0 38.0 1.0
OG1 L:THR17 4.1 37.7 1.0
N L:ASN18 4.3 31.2 1.0
CA L:ASN18 4.4 34.3 1.0
N L:VAL19 4.4 30.0 1.0
CA L:VAL19 4.5 29.5 1.0
CB L:THR17 4.5 36.0 1.0
CA L:LEU72 4.6 32.4 1.0
CG1 L:VAL19 4.7 27.3 1.0
O L:LEU72 4.7 38.8 1.0
CB L:ASN18 4.8 37.1 1.0
O L:SER71 4.9 24.1 1.0
C L:THR17 5.0 37.2 1.0

Calcium binding site 10 out of 10 in 5mki

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Calcium binding site 10 out of 10 in the Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 10 of Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Ca101

b:38.2
occ:0.66
O M:HOH227 2.4 37.9 1.0
OE2 M:GLU56 2.5 43.4 1.0
OE1 M:GLU56 2.8 35.6 1.0
CD M:GLU56 3.0 41.5 1.0
CG M:GLU56 4.5 41.2 1.0
O M:HOH210 4.8 42.1 1.0
O M:HOH222 4.8 51.4 1.0
O M:HOH213 5.0 37.2 1.0
NZ M:LYS48 5.0 48.0 1.0

Reference:

A.D.Nikulin, N.V.Lekontseva, S.V.Tishchenko. Crystal Structure of Smap (Lsm) Protein From Methanococcus Vannielii To Be Published.
Page generated: Sat Dec 12 05:38:05 2020

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